Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/g/gromacs/gromacs_2020.6-2_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/gromacs-2020.6-2x0n9xmab/gromacs_2020.6-2_amd64.buildinfo Get source package info: gromacs=2020.6-2 Source URL: http://snapshot.notset.fr/mr/package/gromacs/2020.6-2/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=adduser=3.118 autoconf=2.69-14 automake=1:1.16.3-2 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=11 base-passwd=3.5.49 bash=5.1-2+b1 binutils=2.35.2-2 binutils-common=2.35.2-2 binutils-x86-64-linux-gnu=2.35.2-2 bsdextrautils=2.36.1-7 bsdutils=1:2.36.1-7 build-essential=12.9 bzip2=1.0.8-4 chrpath=0.16-2+b1 cmake=3.18.4-2 cmake-data=3.18.4-2 coreutils=8.32-4+b1 cpp=4:10.2.1-1 cpp-10=10.2.1-6 dash=0.5.11+git20210120+802ebd4-1 debconf=1.5.76 debhelper=13.3.4 debianutils=4.11.2 dh-autoreconf=20 dh-strip-nondeterminism=1.11.0-1 diffutils=1:3.7-5 distro-info-data=0.46 dpkg=1.20.7.1 dpkg-dev=1.20.7.1 dwz=0.14-1 file=1:5.39-3 findutils=4.8.0-1 g++=4:10.2.1-1 g++-10=10.2.1-6 gcc=4:10.2.1-1 gcc-10=10.2.1-6 gcc-10-base=10.2.1-6 gettext=0.21-4 gettext-base=0.21-4 gfortran=4:10.2.1-1 gfortran-10=10.2.1-6 grep=3.6-1 groff-base=1.22.4-6 gzip=1.10-4 hostname=3.23 hwloc-nox=2.4.1+dfsg-1 ibverbs-providers=33.1-1 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-10 libarchive-zip-perl=1.68-1 libarchive13=3.4.3-2+b1 libasan6=10.2.1-6 libatomic1=10.2.1-6 libattr1=1:2.4.48-6 libaudit-common=1:3.0-2 libaudit1=1:3.0-2 libbinutils=2.35.2-2 libblas-dev=3.9.0-3 libblas3=3.9.0-3 libblkid1=2.36.1-7 libboost-dev=1.74.0.3 libboost1.74-dev=1.74.0-9 libbrotli1=1.0.9-2+b2 libbsd0=0.11.3-1 libbz2-1.0=1.0.8-4 libc-bin=2.31-10 libc-dev-bin=2.31-10 libc6=2.31-10 libc6-dev=2.31-10 libcap-ng0=0.7.9-2.2+b1 libcbor0=0.5.0+dfsg-2 libcc1-0=10.2.1-6 libcom-err2=1.46.2-1 libcrypt-dev=1:4.4.18-2 libcrypt1=1:4.4.18-2 libctf-nobfd0=2.35.2-2 libctf0=2.35.2-2 libcurl4=7.74.0-1.1 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.257 libdebhelper-perl=13.3.4 libdpkg-perl=1.20.7.1 libedit2=3.1-20191231-2+b1 libelf1=0.183-3 libevent-2.1-7=2.1.12-stable-1 libevent-core-2.1-7=2.1.12-stable-1 libevent-dev=2.1.12-stable-1 libevent-extra-2.1-7=2.1.12-stable-1 libevent-openssl-2.1-7=2.1.12-stable-1 libevent-pthreads-2.1-7=2.1.12-stable-1 libexpat1=2.2.10-2 libfabric1=1.11.0-2 libffi7=3.3-6 libfftw3-bin=3.3.8-2 libfftw3-dev=3.3.8-2 libfftw3-double3=3.3.8-2 libfftw3-long3=3.3.8-2 libfftw3-quad3=3.3.8-2 libfftw3-single3=3.3.8-2 libfido2-1=1.6.0-2 libfile-stripnondeterminism-perl=1.11.0-1 libgcc-10-dev=10.2.1-6 libgcc-s1=10.2.1-6 libgcrypt20=1.8.7-3 libgdbm-compat4=1.19-2 libgdbm6=1.19-2 libgfortran-10-dev=10.2.1-6 libgfortran5=10.2.1-6 libgmp10=2:6.2.1+dfsg-1 libgnutls30=3.7.1-1 libgomp1=10.2.1-6 libgpg-error0=1.38-2 libgssapi-krb5-2=1.18.3-4 libhogweed6=3.7-2.1 libhwloc-dev=2.4.1+dfsg-1 libhwloc-plugins=2.4.1+dfsg-1 libhwloc15=2.4.1+dfsg-1 libibverbs-dev=33.1-1 libibverbs1=33.1-1 libicu67=67.1-6 libidn2-0=2.3.0-5 libisl23=0.23-1 libitm1=10.2.1-6 libjs-jquery=3.5.1+dfsg+~3.5.5-7 libjs-jquery-ui=1.12.1+dfsg-8 libjsoncpp24=1.9.4-4 libk5crypto3=1.18.3-4 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-4 libkrb5support0=1.18.3-4 liblapack-dev=3.9.0-3 liblapack3=3.9.0-3 libldap-2.4-2=2.4.57+dfsg-2 liblsan0=10.2.1-6 libltdl-dev=2.4.6-15 libltdl7=2.4.6-15 liblz4-1=1.9.3-1 liblzma5=5.2.5-2 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmd0=1.0.3-3 libmount1=2.36.1-7 libmpc3=1.2.0-1 libmpdec3=2.5.1-2 libmpfr6=4.1.0-3 libmpich-dev=3.4.1-3 libmpich12=3.4.1-3 libncurses6=6.2+20201114-2 libncursesw6=6.2+20201114-2 libnettle8=3.7-2.1 libnghttp2-14=1.43.0-1 libnl-3-200=3.4.0-1+b1 libnl-3-dev=3.4.0-1+b1 libnl-route-3-200=3.4.0-1+b1 libnl-route-3-dev=3.4.0-1+b1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnuma-dev=2.0.12-1+b1 libnuma1=2.0.12-1+b1 libopenmpi-dev=4.1.0-8 libopenmpi3=4.1.0-8 libp11-kit0=0.23.22-1 libpam-modules=1.4.0-7 libpam-modules-bin=1.4.0-7 libpam-runtime=1.4.0-7 libpam0g=1.4.0-7 libpciaccess0=0.16-1 libpcre2-8-0=10.36-2 libpcre3=2:8.39-13 libperl5.32=5.32.1-3 libpipeline1=1.5.3-1 libpmix-dev=4.0.0-4 libpmix2=4.0.0-4 libprocps8=2:3.3.17-4 libpsl5=0.21.0-1.2 libpsm-infinipath1=3.3+20.604758e7-6.1 libpsm2-2=11.2.185-1 libpthread-stubs0-dev=0.4-1 libpython3-stdlib=3.9.2-2 libpython3.9-minimal=3.9.2-1 libpython3.9-stdlib=3.9.2-1 libquadmath0=10.2.1-6 librdmacm1=33.1-1 libreadline8=8.1-1 librhash0=1.4.1-2 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg-2.1 libsasl2-modules-db=2.1.27+dfsg-2.1 libseccomp2=2.5.1-1 libselinux1=3.1-3 libsemanage-common=3.1-1 libsemanage1=3.1-1+b2 libsepol1=3.1-1 libsigsegv2=2.13-1 libslurm36=20.11.4-1 libsmartcols1=2.36.1-7 libsqlite3-0=3.34.1-3 libssh2-1=1.9.0-3 libssl1.1=1.1.1k-1 libstdc++-10-dev=10.2.1-6 libstdc++6=10.2.1-6 libsub-override-perl=0.09-2 libsystemd0=247.3-3 libtasn1-6=4.16.0-2 libtinfo6=6.2+20201114-2 libtirpc-common=1.3.1-1 libtirpc-dev=1.3.1-1 libtirpc3=1.3.1-1 libtool=2.4.6-15 libtsan0=10.2.1-6 libubsan1=10.2.1-6 libuchardet0=0.0.7-1 libucx0=1.10.0~rc1-7 libudev1=247.3-3 libunistring2=0.9.10-4 libuuid1=2.36.1-7 libuv1=1.40.0-1 libx11-6=2:1.7.0-2 libx11-data=2:1.7.0-2 libx11-dev=2:1.7.0-2 libxau-dev=1:1.0.9-1 libxau6=1:1.0.9-1 libxcb1=1.14-3 libxcb1-dev=1.14-3 libxdmcp-dev=1:1.1.2-3 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.3-1.1 libxml2=2.9.10+dfsg-6.3+b1 libxnvctrl0=460.56-1 libzstd1=1.4.8+dfsg-2.1 linux-libc-dev=5.10.26-1 login=1:4.8.1-1 lsb-base=11.1.0 lsb-release=11.1.0 m4=1.4.18-5 make=4.3-4 man-db=2.9.4-2 mawk=1.3.4.20200120-2 media-types=4.0.0 mpich=3.4.1-3 ncurses-base=6.2+20201114-2 ncurses-bin=6.2+20201114-2 ocl-icd-libopencl1=2.2.14-2 openmpi-bin=4.1.0-8 openmpi-common=4.1.0-8 openssh-client=1:8.4p1-5 passwd=1:4.8.1-1 patch=2.7.6-7 perl=5.32.1-3 perl-base=5.32.1-3 perl-modules-5.32=5.32.1-3 po-debconf=1.0.21+nmu1 procps=2:3.3.17-4 python3=3.9.2-2 python3-minimal=3.9.2-2 python3.9=3.9.2-1 python3.9-minimal=3.9.2-1 readline-common=8.1-1 sed=4.7-1 sensible-utils=0.0.14 sysvinit-utils=2.96-6 tar=1.34+dfsg-1 tzdata=2021a-1 util-linux=2.36.1-7 x11proto-dev=2020.1-1 xorg-sgml-doctools=1:1.11-1.1 xtrans-dev=1.4.0-1 xz-utils=5.2.5-2 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210330T090157Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d gromacs=2020.6-2 && mkdir -p /build/gromacs-5atmZb && dpkg-source --no-check -x /*.dsc /build/gromacs-5atmZb/gromacs-2020.6 && chown -R builduser:builduser /build/gromacs-5atmZb" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/gromacs-5atmZb/gromacs-2020.6 && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1616993103" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/gromacs-5atmZb /tmp/gromacs-2020.6-2x0n9xmab bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20210330T090157Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.b22wTBKfhG as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.b22wTBKfhG Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-7). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20210330T090157Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210330T090157Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (839 kB/s) Selecting previously unselected package libfakeroot:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4663 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-10) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210330T090157Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.b22wTBKfhG Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20210330T090157Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Fetched 22.6 MB in 20s (1154 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.b22wTBKfhG I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d gromacs=2020.6-2 && mkdir -p /build/gromacs-5atmZb && dpkg-source --no-check -x /*.dsc /build/gromacs-5atmZb/gromacs-2020.6 && chown -R builduser:builduser /build/gromacs-5atmZb"' exec /tmp/mmdebstrap.b22wTBKfhG Reading package lists... NOTICE: 'gromacs' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/debichem-team/gromacs.git Please use: git clone https://salsa.debian.org/debichem-team/gromacs.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 77.8 MB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main gromacs 2020.6-2 (dsc) [2948 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main gromacs 2020.6-2 (tar) [48.5 MB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main gromacs 2020.6-2 (tar) [29.2 MB] Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main gromacs 2020.6-2 (diff) [38.3 kB] Fetched 77.8 MB in 1min 3s (1230 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'gromacs_2020.6-2.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting gromacs in /build/gromacs-5atmZb/gromacs-2020.6 dpkg-source: info: unpacking gromacs_2020.6.orig.tar.gz dpkg-source: info: unpacking gromacs_2020.6.orig-regressiontests.tar.gz dpkg-source: info: unpacking gromacs_2020.6-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying disable-listed-forces-test.patch dpkg-source: info: applying arm64-disable-numa-test.patch dpkg-source: info: applying readme.patch dpkg-source: info: applying copyright-file.patch dpkg-source: info: applying disable-cpuinfotest.patch dpkg-source: info: applying mdrun-test-timeout.patch dpkg-source: info: applying local-mathjax.patch dpkg-source: info: applying mpi-tests-localhost.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/gromacs-5atmZb/gromacs-2020.6 && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1616993103" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.b22wTBKfhG dpkg-buildpackage: info: source package gromacs dpkg-buildpackage: info: source version 2020.6-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nicholas Breen dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh_testdir dh_testroot rm -rf build docs/doxygen/*.pyc dh_clean build-basic build-mpich build-openmpi build-manual configure-stamp \ debian/gromacs-mpich.README.Debian debian/gromacs-openmpi.README.Debian debian/rules binary-arch dh_testdir (mkdir -p build/basic; cd build/basic; cmake /build/gromacs-5atmZb/gromacs-2020.6 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Debian-2020.6-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=SSE4.1 -DGMX_MPI=OFF -DGMX_X11=ON -DBUILD_SHARED_LIBS=ON -DGMX_INSTALL_LEGACY_API=ON) -- The C compiler identification is GNU 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for NVIDIA GPUs present in the system -- Could not detect NVIDIA GPUs -- No compatible CUDA toolkit found (v5.0+), disabling native GPU acceleration -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable version "2.4.1", minimum required is "1.5") -- Found X11: /usr/include -- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so -- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so - found -- Looking for gethostbyname -- Looking for gethostbyname - found -- Looking for connect -- Looking for connect - found -- Looking for remove -- Looking for remove - found -- Looking for shmat -- Looking for shmat - found -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so - found -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - Intel -- Detected build CPU brand - Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz -- Detected build CPU family - 6 -- Detected build CPU model - 45 -- Detected build CPU stepping - 7 -- Detected build CPU features - aes apic avx clfsh cmov cx8 cx16 htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic -- Disabling RDTSCP support -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - present -- Performing Test C_msse4_1_FLAG_ACCEPTED -- Performing Test C_msse4_1_FLAG_ACCEPTED - Success -- Performing Test C_msse4_1_COMPILE_WORKS -- Performing Test C_msse4_1_COMPILE_WORKS - Success -- Performing Test CXX_msse4_1_FLAG_ACCEPTED -- Performing Test CXX_msse4_1_FLAG_ACCEPTED - Success -- Performing Test CXX_msse4_1_COMPILE_WORKS -- Performing Test CXX_msse4_1_COMPILE_WORKS - Success -- Enabling SSE4.1 SIMD instructions using CXX flags: -msse4.1 -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- pkg-config could not detect fftw3f, trying generic detection -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- Using dynamic plugins (e.g VMD-supported file formats) -- Checking for suitable VMD version -- VMD plugins not found. Path to VMD can be set with VMDDIR. -- Using default binary suffix: "" -- Using default library suffix: "" -- Could not convert sample image, ImageMagick convert can not be used. A possible way to fix it can be found here: https://alexvanderbist.com/2018/fixing-imagick-error-unauthorized Traceback (most recent call last): File "", line 1, in ModuleNotFoundError: No module named 'pygments' -- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE pygments) (Required is at least version "1.6.1") -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success -- Performing Test HAS_NO_REDUNDANT_MOVE -- Performing Test HAS_NO_REDUNDANT_MOVE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Performing Test HAS_NO_CLASS_MEMACCESS -- Performing Test HAS_NO_CLASS_MEMACCESS - Success -- Check if the system is big endian -- Searching 16 bit integer -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- Looking for inttypes.h -- Looking for inttypes.h - found -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Doxygen not found. Documentation targets will not be generated. -- Configuring done -- Generating done -- Build files have been written to: /build/gromacs-5atmZb/gromacs-2020.6/build/basic (mkdir -p build/basic-dp; cd build/basic-dp; cmake /build/gromacs-5atmZb/gromacs-2020.6 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Debian-2020.6-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=SSE4.1 -DGMX_MPI=OFF -DGMX_X11=ON -DBUILD_SHARED_LIBS=ON -DGMX_DOUBLE=ON) -- The C compiler identification is GNU 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Warning at cmake/gmxManageGPU.cmake:53 (message): GPU acceleration is not available in double precision, disabled! Call Stack (most recent call first): CMakeLists.txt:217 (include) -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable version "2.4.1", minimum required is "1.5") -- Found X11: /usr/include -- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so -- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so - found -- Looking for gethostbyname -- Looking for gethostbyname - found -- Looking for connect -- Looking for connect - found -- Looking for remove -- Looking for remove - found -- Looking for shmat -- Looking for shmat - found -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so - found -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - Intel -- Detected build CPU brand - Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz -- Detected build CPU family - 6 -- Detected build CPU model - 45 -- Detected build CPU stepping - 7 -- Detected build CPU features - aes apic avx clfsh cmov cx8 cx16 htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic -- Disabling RDTSCP support -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - present -- Performing Test C_msse4_1_FLAG_ACCEPTED -- Performing Test C_msse4_1_FLAG_ACCEPTED - Success -- Performing Test C_msse4_1_COMPILE_WORKS -- Performing Test C_msse4_1_COMPILE_WORKS - Success -- Performing Test CXX_msse4_1_FLAG_ACCEPTED -- Performing Test CXX_msse4_1_FLAG_ACCEPTED - Success -- Performing Test CXX_msse4_1_COMPILE_WORKS -- Performing Test CXX_msse4_1_COMPILE_WORKS - Success -- Enabling SSE4.1 SIMD instructions using CXX flags: -msse4.1 -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- pkg-config could not detect fftw3, trying generic detection -- Looking for fftw_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- Using dynamic plugins (e.g VMD-supported file formats) -- Checking for suitable VMD version -- VMD plugins not found. Path to VMD can be set with VMDDIR. -- Using default binary suffix: "_d" -- Using default library suffix: "_d" -- Could not convert sample image, ImageMagick convert can not be used. A possible way to fix it can be found here: https://alexvanderbist.com/2018/fixing-imagick-error-unauthorized Traceback (most recent call last): File "", line 1, in ModuleNotFoundError: No module named 'pygments' -- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE pygments) (Required is at least version "1.6.1") -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success -- Performing Test HAS_NO_REDUNDANT_MOVE -- Performing Test HAS_NO_REDUNDANT_MOVE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Performing Test HAS_NO_CLASS_MEMACCESS -- Performing Test HAS_NO_CLASS_MEMACCESS - Success -- Check if the system is big endian -- Searching 16 bit integer -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- Looking for inttypes.h -- Looking for inttypes.h - found -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Doxygen not found. Documentation targets will not be generated. -- Configuring done -- Generating done -- Build files have been written to: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp (mkdir -p build/mpich; cd build/mpich; CC=/usr/bin/mpicc.mpich CXX=/usr/bin/mpicxx.mpich cmake \ /build/gromacs-5atmZb/gromacs-2020.6 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Debian-2020.6-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=SSE4.1 -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DMPIEXEC="/usr/bin/mpiexec.mpich" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_BINARY_SUFFIX="_mpi.mpich" -DGMX_LIBS_SUFFIX="_mpi.mpich") -- The C compiler identification is GNU 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/mpicc.mpich - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/mpicxx.mpich - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for NVIDIA GPUs present in the system -- Could not detect NVIDIA GPUs -- No compatible CUDA toolkit found (v5.0+), disabling native GPU acceleration -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Checking for MPI_IN_PLACE -- Performing Test MPI_IN_PLACE_COMPILE_OK -- Performing Test MPI_IN_PLACE_COMPILE_OK - Success -- Checking for MPI_IN_PLACE - yes -- Defaulting to building static libraries -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable version "2.4.1", minimum required is "1.5") -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so - found -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - Intel -- Detected build CPU brand - Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz -- Detected build CPU family - 6 -- Detected build CPU model - 45 -- Detected build CPU stepping - 7 -- Detected build CPU features - aes apic avx clfsh cmov cx8 cx16 htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic -- Disabling RDTSCP support -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - present -- Performing Test C_msse4_1_FLAG_ACCEPTED -- Performing Test C_msse4_1_FLAG_ACCEPTED - Success -- Performing Test C_msse4_1_COMPILE_WORKS -- Performing Test C_msse4_1_COMPILE_WORKS - Success -- Performing Test CXX_msse4_1_FLAG_ACCEPTED -- Performing Test CXX_msse4_1_FLAG_ACCEPTED - Success -- Performing Test CXX_msse4_1_COMPILE_WORKS -- Performing Test CXX_msse4_1_COMPILE_WORKS - Success -- Enabling SSE4.1 SIMD instructions using CXX flags: -msse4.1 -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- pkg-config could not detect fftw3f, trying generic detection -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.) -- Not using dynamic plugins (e.g VMD-supported file formats) -- Using manually set binary suffix: "_mpi.mpich" -- Using manually set library suffix: "_mpi.mpich" -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success -- Performing Test HAS_NO_REDUNDANT_MOVE -- Performing Test HAS_NO_REDUNDANT_MOVE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Performing Test HAS_NO_CLASS_MEMACCESS -- Performing Test HAS_NO_CLASS_MEMACCESS - Success -- Check if the system is big endian -- Searching 16 bit integer -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- Looking for inttypes.h -- Looking for inttypes.h - found -- Configuring done -- Generating done -- Build files have been written to: /build/gromacs-5atmZb/gromacs-2020.6/build/mpich (mkdir -p build/mpich-dp; cd build/mpich-dp; CC=/usr/bin/mpicc.mpich CXX=/usr/bin/mpicxx.mpich cmake \ /build/gromacs-5atmZb/gromacs-2020.6 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Debian-2020.6-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=SSE4.1 -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DMPIEXEC="/usr/bin/mpiexec.mpich" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d.mpich" -DGMX_LIBS_SUFFIX="_mpi_d.mpich") -- The C compiler identification is GNU 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/mpicc.mpich - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/mpicxx.mpich - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Warning at cmake/gmxManageGPU.cmake:53 (message): GPU acceleration is not available in double precision, disabled! Call Stack (most recent call first): CMakeLists.txt:217 (include) -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Checking for MPI_IN_PLACE -- Performing Test MPI_IN_PLACE_COMPILE_OK -- Performing Test MPI_IN_PLACE_COMPILE_OK - Success -- Checking for MPI_IN_PLACE - yes -- Defaulting to building static libraries -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable version "2.4.1", minimum required is "1.5") -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so - found -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - Intel -- Detected build CPU brand - Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz -- Detected build CPU family - 6 -- Detected build CPU model - 45 -- Detected build CPU stepping - 7 -- Detected build CPU features - aes apic avx clfsh cmov cx8 cx16 htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic -- Disabling RDTSCP support -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - present -- Performing Test C_msse4_1_FLAG_ACCEPTED -- Performing Test C_msse4_1_FLAG_ACCEPTED - Success -- Performing Test C_msse4_1_COMPILE_WORKS -- Performing Test C_msse4_1_COMPILE_WORKS - Success -- Performing Test CXX_msse4_1_FLAG_ACCEPTED -- Performing Test CXX_msse4_1_FLAG_ACCEPTED - Success -- Performing Test CXX_msse4_1_COMPILE_WORKS -- Performing Test CXX_msse4_1_COMPILE_WORKS - Success -- Enabling SSE4.1 SIMD instructions using CXX flags: -msse4.1 -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- pkg-config could not detect fftw3, trying generic detection -- Looking for fftw_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.) -- Not using dynamic plugins (e.g VMD-supported file formats) -- Using manually set binary suffix: "_mpi_d.mpich" -- Using manually set library suffix: "_mpi_d.mpich" -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success -- Performing Test HAS_NO_REDUNDANT_MOVE -- Performing Test HAS_NO_REDUNDANT_MOVE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Performing Test HAS_NO_CLASS_MEMACCESS -- Performing Test HAS_NO_CLASS_MEMACCESS - Success -- Check if the system is big endian -- Searching 16 bit integer -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- Looking for inttypes.h -- Looking for inttypes.h - found -- Configuring done -- Generating done -- Build files have been written to: /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp (mkdir -p build/openmpi; cd build/openmpi; CC=/usr/bin/mpicc.openmpi CXX=/usr/bin/mpicxx.openmpi cmake \ /build/gromacs-5atmZb/gromacs-2020.6 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Debian-2020.6-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=SSE4.1 -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DCMAKE_EXE_LINKER_FLAGS="-L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now" -DMPIEXEC="/usr/bin/mpiexec.openmpi" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_BINARY_SUFFIX="_mpi.openmpi" -DGMX_LIBS_SUFFIX="_mpi.openmpi") -- The C compiler identification is GNU 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/mpicc.openmpi - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/mpicxx.openmpi - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for NVIDIA GPUs present in the system -- Could not detect NVIDIA GPUs -- No compatible CUDA toolkit found (v5.0+), disabling native GPU acceleration -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Checking for MPI_IN_PLACE -- Performing Test MPI_IN_PLACE_COMPILE_OK -- Performing Test MPI_IN_PLACE_COMPILE_OK - Success -- Checking for MPI_IN_PLACE - yes -- Defaulting to building static libraries -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable version "2.4.1", minimum required is "1.5") -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so - found -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - Intel -- Detected build CPU brand - Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz -- Detected build CPU family - 6 -- Detected build CPU model - 45 -- Detected build CPU stepping - 7 -- Detected build CPU features - aes apic avx clfsh cmov cx8 cx16 htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic -- Disabling RDTSCP support -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - present -- Performing Test C_msse4_1_FLAG_ACCEPTED -- Performing Test C_msse4_1_FLAG_ACCEPTED - Success -- Performing Test C_msse4_1_COMPILE_WORKS -- Performing Test C_msse4_1_COMPILE_WORKS - Success -- Performing Test CXX_msse4_1_FLAG_ACCEPTED -- Performing Test CXX_msse4_1_FLAG_ACCEPTED - Success -- Performing Test CXX_msse4_1_COMPILE_WORKS -- Performing Test CXX_msse4_1_COMPILE_WORKS - Success -- Enabling SSE4.1 SIMD instructions using CXX flags: -msse4.1 -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- pkg-config could not detect fftw3f, trying generic detection -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.) -- Not using dynamic plugins (e.g VMD-supported file formats) -- Using manually set binary suffix: "_mpi.openmpi" -- Using manually set library suffix: "_mpi.openmpi" -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success -- Performing Test HAS_NO_REDUNDANT_MOVE -- Performing Test HAS_NO_REDUNDANT_MOVE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Performing Test HAS_NO_CLASS_MEMACCESS -- Performing Test HAS_NO_CLASS_MEMACCESS - Success -- Check if the system is big endian -- Searching 16 bit integer -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- Looking for inttypes.h -- Looking for inttypes.h - found -- Configuring done -- Generating done -- Build files have been written to: /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi (mkdir -p build/openmpi-dp; cd build/openmpi-dp; CC=/usr/bin/mpicc.openmpi CXX=/usr/bin/mpicxx.openmpi cmake \ /build/gromacs-5atmZb/gromacs-2020.6 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Debian-2020.6-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=SSE4.1 -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DCMAKE_EXE_LINKER_FLAGS="-L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now" -DMPIEXEC="/usr/bin/mpiexec.openmpi" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d.openmpi" -DGMX_LIBS_SUFFIX="_mpi_d.openmpi") -- The C compiler identification is GNU 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/mpicc.openmpi - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/mpicxx.openmpi - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Warning at cmake/gmxManageGPU.cmake:53 (message): GPU acceleration is not available in double precision, disabled! Call Stack (most recent call first): CMakeLists.txt:217 (include) -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Checking for MPI_IN_PLACE -- Performing Test MPI_IN_PLACE_COMPILE_OK -- Performing Test MPI_IN_PLACE_COMPILE_OK - Success -- Checking for MPI_IN_PLACE - yes -- Defaulting to building static libraries -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable version "2.4.1", minimum required is "1.5") -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so - found -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - Intel -- Detected build CPU brand - Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz -- Detected build CPU family - 6 -- Detected build CPU model - 45 -- Detected build CPU stepping - 7 -- Detected build CPU features - aes apic avx clfsh cmov cx8 cx16 htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic -- Disabling RDTSCP support -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - present -- Performing Test C_msse4_1_FLAG_ACCEPTED -- Performing Test C_msse4_1_FLAG_ACCEPTED - Success -- Performing Test C_msse4_1_COMPILE_WORKS -- Performing Test C_msse4_1_COMPILE_WORKS - Success -- Performing Test CXX_msse4_1_FLAG_ACCEPTED -- Performing Test CXX_msse4_1_FLAG_ACCEPTED - Success -- Performing Test CXX_msse4_1_COMPILE_WORKS -- Performing Test CXX_msse4_1_COMPILE_WORKS - Success -- Enabling SSE4.1 SIMD instructions using CXX flags: -msse4.1 -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- pkg-config could not detect fftw3, trying generic detection -- Looking for fftw_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.) -- Not using dynamic plugins (e.g VMD-supported file formats) -- Using manually set binary suffix: "_mpi_d.openmpi" -- Using manually set library suffix: "_mpi_d.openmpi" -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success -- Performing Test HAS_NO_REDUNDANT_MOVE -- Performing Test HAS_NO_REDUNDANT_MOVE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Performing Test HAS_NO_CLASS_MEMACCESS -- Performing Test HAS_NO_CLASS_MEMACCESS - Success -- Check if the system is big endian -- Searching 16 bit integer -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- Looking for inttypes.h -- Looking for inttypes.h - found -- Configuring done -- Generating done -- Build files have been written to: /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp touch configure-stamp dh_testdir /usr/bin/make -j4 -C build/basic make[1]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/cmake -S/build/gromacs-5atmZb/gromacs-2020.6 -B/build/gromacs-5atmZb/gromacs-2020.6/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-5atmZb/gromacs-2020.6/build/basic/CMakeFiles /build/gromacs-5atmZb/gromacs-2020.6/build/basic//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/selection /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/CMakeFiles/release-version-info.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color= Scanning dependencies of target release-version-info make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.6-Debian-2020.6-2 -D PROJECT_SOURCE_DIR=/build/gromacs-5atmZb/gromacs-2020.6 -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/build/gromacs-5atmZb/gromacs-2020.6/build/basic/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/gromacs-5atmZb/gromacs-2020.6/build/basic/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2020.6-2 -P /build/gromacs-5atmZb/gromacs-2020.6/cmake/gmxGenerateVersionInfoRelease.cmake Scanning dependencies of target lmfit_objlib make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build Scanning dependencies of target scanner make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++14 -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit/lmmin.cpp make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/parser.cpp make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 0%] Built target release-version-info Scanning dependencies of target thread_mpi /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/errhandler.cpp Scanning dependencies of target tng_io_obj make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/bwlzh.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/tmpi_malloc.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/atomic.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/lock.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/pthreads.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/system_error.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/bwt.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/alltoall.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/p2p_protocol.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/coder.c make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 0%] Built target lmfit_objlib cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/dict.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/fixpoint.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/huffman.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/barrier.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/p2p_send_recv.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/huffmem.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src 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-ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/comm.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/reduce.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/rle.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/tng_compress.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/event.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/reduce_fast.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/gather.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/scatter.cpp cd 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-ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/tmpi_init.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/topology.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/list.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/type.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/warnmalloc.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/widemuldiv.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/xtc2.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/xtc3.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/lib/tng_io.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/scanner.cpp make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 1%] Built target scanner cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/scan.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/lib/md5.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/numa_malloc.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/once.cpp /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/linearalgebra /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= Scanning dependencies of target linearalgebra make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra/eigensolver.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra/gmx_arpack.cpp make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 4%] Built target thread_mpi /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/modularsimulator /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color= Scanning dependencies of target modularsimulator make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/checkpointhelper.cpp /usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/fileio /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/fileio/CMakeFiles/vmddlopen.dir/DependInfo.cmake --color= Scanning dependencies of target vmddlopen make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/fileio && /usr/bin/c++ -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/vmddlopen.dir/__/__/external/vmd_molfile/vmddlopen.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/vmd_molfile/vmddlopen.cpp make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 4%] Built target vmddlopen /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun_objlib make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/mdrun.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/compositesimulatorelement.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/computeglobalselement.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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/build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra/nrjac.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/energyelement.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/energyelement.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/forceelement.cpp make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 6%] Built target tng_io_obj /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make 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-I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/3dview.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/view/3dview.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation 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'/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/gromacs-5atmZb/gromacs-2020.6/build/basic/VersionInfo.cmake -D VERSION_CMAKEIN=/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/gromacs-5atmZb/gromacs-2020.6/cmake/gmxConfigureVersionInfo.cmake cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs 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-I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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/build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_prune.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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-fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem 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/build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxana/gmx_angle.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxana/gmx_awh.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxana/gmx_bar.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxana/gmx_bundle.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxana/gmx_chi.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxana/gmx_cluster.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxana/gmx_clustsize.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -c 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/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxana/gmx_covar.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxana/gmx_current.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxana/gmx_density.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxana/gmx_densmap.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxana/gmx_densorder.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -c 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/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxana/gmx_dos.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -c 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/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxana/gmx_wham.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxana/gmx_wheel.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxana/gmx_xpm2ps.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxana/hxprops.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxana/nrama.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxana/nsfactor.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxana/powerspect.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxana/pp2shift.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -c 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/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxana/sfactor.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxana/thermochemistry.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -c 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/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/convparm.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -c 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/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/fflibutil.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/gen_ad.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/gen_maxwell_velocities.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/gen_vsite.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/genconf.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/genhydro.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/genion.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/genrestr.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/gmxcpp.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/gpp_atomtype.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/gpp_bond_atomtype.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/gpp_nextnb.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/grompp.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/h_db.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -c 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/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/hizzie.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/insert_molecules.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/nm2type.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/pdb2gmx.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/pdb2top.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/pgutil.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/readir.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/readpull.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/readrot.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/resall.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/solvate.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/specbond.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/ter_db.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -c 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/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/topio.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/toppush.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -c 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/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/toputil.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -c 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/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/xlate.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/correlationfunctions/autocorr.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o -c 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/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/correlationfunctions/gmx_lmcurve.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -c 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-I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fft/fft.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fft/fft5d.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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-I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fft/fft_fftw3.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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selection/CMakeFiles/scanner.dir/scanner.cpp.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o 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../../lib/libgromacs.so.5 ../../lib/libgromacs.so make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 98%] Built target libgromacs /usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend /usr/bin/make -f src/api/cpp/CMakeFiles/gmxapi.dir/build.make src/api/cpp/CMakeFiles/gmxapi.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/share/template /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/share/template /build/gromacs-5atmZb/gromacs-2020.6/build/basic/share/template/CMakeFiles/template.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/CMakeFiles/gmxapi.dir/DependInfo.cmake --color= Scanning dependencies of target template make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/share/template && /usr/bin/c++ -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -std=c++14 -o CMakeFiles/template.dir/template.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/share/template/template.cpp Scanning dependencies of target gmx make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmx.dir/gmx.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/gmx.cpp Scanning dependencies of target gmxapi cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmx.dir/legacymodules.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/legacymodules.cpp make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/api/cpp/CMakeFiles/gmxapi.dir/build.make src/api/cpp/CMakeFiles/gmxapi.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 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/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/gmxapi.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/md.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/md.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmx.dir/gmx.cpp.o CMakeFiles/gmx.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o CMakeFiles/view_objlib.dir/view/3dview.cpp.o CMakeFiles/view_objlib.dir/view/buttons.cpp.o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o CMakeFiles/view_objlib.dir/view/filter.cpp.o CMakeFiles/view_objlib.dir/view/logo.cpp.o CMakeFiles/view_objlib.dir/view/manager.cpp.o CMakeFiles/view_objlib.dir/view/molps.cpp.o CMakeFiles/view_objlib.dir/view/nleg.cpp.o CMakeFiles/view_objlib.dir/view/nmol.cpp.o CMakeFiles/view_objlib.dir/view/popup.cpp.o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o CMakeFiles/view_objlib.dir/view/view.cpp.o CMakeFiles/view_objlib.dir/view/x11.cpp.o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o CMakeFiles/view_objlib.dir/view/xmb.cpp.o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -o ../../bin/gmx ../../lib/libgromacs.so.5.0.0 /usr/lib/x86_64-linux-gnu/libX11.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 98%] Built target gmx cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/mdmodule.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/mdmodule.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/share/template && /usr/bin/cmake -E cmake_link_script CMakeFiles/template.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/template.dir/template.cpp.o -o ../../bin/template ../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 98%] Built target template cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/mdsignals.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/mdsignals.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp && /usr/bin/c++ 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-ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/version.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/version.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC 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/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tpr.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmxapi.so.0 -o ../../../lib/libgmxapi.so.0.1.0 CMakeFiles/gmxapi.dir/context.cpp.o CMakeFiles/gmxapi.dir/exceptions.cpp.o CMakeFiles/gmxapi.dir/gmxapi.cpp.o CMakeFiles/gmxapi.dir/md.cpp.o CMakeFiles/gmxapi.dir/mdmodule.cpp.o CMakeFiles/gmxapi.dir/mdsignals.cpp.o CMakeFiles/gmxapi.dir/session.cpp.o CMakeFiles/gmxapi.dir/status.cpp.o CMakeFiles/gmxapi.dir/system.cpp.o CMakeFiles/gmxapi.dir/version.cpp.o CMakeFiles/gmxapi.dir/workflow.cpp.o CMakeFiles/gmxapi.dir/tpr.cpp.o ../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libgmxapi.so.0.1.0 ../../../lib/libgmxapi.so.0 ../../../lib/libgmxapi.so make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [100%] Built target gmxapi make[2]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/cmake -E cmake_progress_start /build/gromacs-5atmZb/gromacs-2020.6/build/basic/CMakeFiles 0 make[1]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -j4 -C build/basic-dp make[1]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/cmake -S/build/gromacs-5atmZb/gromacs-2020.6 -B/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/CMakeFiles 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/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/selection /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color= Scanning dependencies of target lmfit_objlib make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++14 -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit/lmmin.cpp Scanning dependencies of target release-version-info make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.6-Debian-2020.6-2 -D PROJECT_SOURCE_DIR=/build/gromacs-5atmZb/gromacs-2020.6 -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2020.6-2 -P /build/gromacs-5atmZb/gromacs-2020.6/cmake/gmxGenerateVersionInfoRelease.cmake Scanning dependencies of target scanner make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/parser.cpp make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' Scanning dependencies of target thread_mpi make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/errhandler.cpp [ 0%] Built target release-version-info cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/tmpi_malloc.cpp /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/atomic.cpp Scanning dependencies of target tng_io_obj make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/bwlzh.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/lock.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/pthreads.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/system_error.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/alltoall.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/bwt.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/p2p_protocol.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/coder.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/barrier.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/p2p_send_recv.cpp make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 1%] Built target lmfit_objlib cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/bcast.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/p2p_wait.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/scanner.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/dict.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/fixpoint.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/huffman.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/collective.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/profile.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/comm.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/huffmem.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/reduce.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/lz77.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/event.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/reduce_fast.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/gather.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/scatter.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/merge_sort.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast 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-I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/rle.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/tng_compress.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/tmpi_init.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/vals16.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/topology.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/warnmalloc.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/widemuldiv.c cd 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/build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/list.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/type.cpp make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 1%] Built target scanner /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/linearalgebra /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= Scanning dependencies of target linearalgebra make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra/eigensolver.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/xtc3.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/lib/tng_io.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation 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-I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/scan.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra/matrix.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/numa_malloc.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/once.cpp make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 4%] Built target thread_mpi /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/modularsimulator /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color= Scanning dependencies of target modularsimulator make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/checkpointhelper.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra/nrjac.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/compositesimulatorelement.cpp /usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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-ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/vmddlopen.dir/__/__/external/vmd_molfile/vmddlopen.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/vmd_molfile/vmddlopen.cpp make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 4%] Built target vmddlopen /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs 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CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/mdrun.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/computeglobalselement.cpp make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 4%] Built target linearalgebra /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make 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/build/gromacs-5atmZb/gromacs-2020.6/src/programs/view/buttons.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/nonbonded_bench.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -g -O2 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CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/propagator.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/shellfcelement.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/shellfcelement.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src 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/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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-isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd 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/build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem 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/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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-msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. 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-ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_prune.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem 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/build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem 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-I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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/usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_prune.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/nbnxm.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/nbnxm_geometry.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/nbnxm_setup.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/pairlist.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c 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/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/editconf.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -c 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/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/gpp_bond_atomtype.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -c 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/build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/gpu_hw_info.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/hardware/gpu_hw_info.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/hardware/hardwaretopology.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/hardware/printhardware.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/hardware/identifyavx512fmaunits.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include 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/build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdrun/legacysimulator.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem 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/build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdrun/mimic.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdrun/minimize.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/tng/include -isystem 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CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o /usr/lib/x86_64-linux-gnu/libhwloc.so -ldl -lrt /usr/lib/x86_64-linux-gnu/libfftw3.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so -lpthread -lm /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblapack.so -lpthread -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs_d.so.5.0.0 ../../lib/libgromacs_d.so.5 ../../lib/libgromacs_d.so make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 98%] Built target libgromacs /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend /usr/bin/make -f src/api/cpp/CMakeFiles/gmxapi.dir/build.make src/api/cpp/CMakeFiles/gmxapi.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/CMakeFiles/gmxapi.dir/DependInfo.cmake --color= Scanning dependencies of target gmx make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmx.dir/gmx.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/gmx.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmx.dir/legacymodules.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/legacymodules.cpp Scanning dependencies of target gmxapi make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/api/cpp/CMakeFiles/gmxapi.dir/build.make src/api/cpp/CMakeFiles/gmxapi.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/context.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/context.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/exceptions.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/exceptions.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp && /usr/bin/c++ 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src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build [ 1%] Built target lmfit_objlib /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/linearalgebra /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 3%] Built target thread_mpi /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend [ 3%] Built target release-version-info make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' make[4]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/fileio /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/fileio/CMakeFiles/vmddlopen.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/modularsimulator 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'/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' make[4]: Nothing to be done for 'src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build'. make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs 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make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' Scanning dependencies of target gtest make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build.make src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/external/googletest/googlemock/gtest && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -Dgtest_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wshadow -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=c++14 -o CMakeFiles/gtest.dir/src/gtest-all.cc.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/src/gtest-all.cc [ 5%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend [ 5%] Built target mdrun_objlib make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/basic 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgtest.so -o ../../../../../lib/libgtest.so CMakeFiles/gtest.dir/src/gtest-all.cc.o -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 65%] Built target gtest /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/external/googletest/googlemock /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/external/googletest/googlemock/CMakeFiles/gmock.dir/DependInfo.cmake --color= Scanning dependencies of target gmock make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/external/googletest/googlemock && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -D_GNU_SOURCE=1 -Dgmock_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 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-Wl,-soname,libgmock.so -o ../../../../lib/libgmock.so CMakeFiles/gmock.dir/src/gmock-all.cc.o -lpthread ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 65%] Built target gmock /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/testutils /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/testutils /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/testutils/CMakeFiles/testutils.dir/DependInfo.cmake --color= Scanning dependencies of target testutils make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f 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/build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/tprfilegenerator.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/tprfilegenerator.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem 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'/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 68%] Built target testutils /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/depend /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/depend /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/depend /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests 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/build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/tests/mpitest.cpp Scanning dependencies of target testutils-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" 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target utility-mpi-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/physicalnodecommunicator_mpi.cpp Scanning dependencies of target mdrun_test_infrastructure make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/energyreader.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 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/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/energycomparison.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libgromacs.so.5.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../lib/libgtest.so -lpthread cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 68%] Built target testutils-mpi-test /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake --color= cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/tests/refdata_tests.cpp Scanning dependencies of target utility-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/alignedallocator.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 68%] Built target utility-mpi-test /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdlib-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/calc_verletbuf.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/constr.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/moduletest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/mdmodulenotification.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/mdmodulenotification.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/tests/testasserts_tests.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/terminationhelper.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/trajectorycomparison.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/arrayref.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/constrtestdata.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/tests/xvgtest_tests.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/constrtestrunners.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-test.dir/interactivetest.cpp.o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libgromacs.so.5.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 69%] Built target testutils-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/ebin.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/trajectoryreader.cpp /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/applied_forces/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/applied_forces/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake --color= Scanning dependencies of target applied_forces-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfitting.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/applied_forces/tests/densityfitting.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/energyoutput.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/mdmodulenotification.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o /usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 69%] Built target mdrun_test_infrastructure /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/onlinehelp/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/onlinehelp/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color= Scanning dependencies of target onlinehelp-test-shared make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/onlinehelp/tests/mock_helptopic.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfittingoptions.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/applied_forces/tests/densityfittingoptions.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o /usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 69%] Built target onlinehelp-test-shared cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/applied_forces/tests/densityfittingamplitudelookup.cpp /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/domdec/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/domdec/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color= Scanning dependencies of target domdec-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/domdec/tests/hashedmap.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/expanded.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/applied_forces/tests/electricfield.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/domdec/tests/localatomsetmanager.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/leapfrog.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/domdec-test.dir/hashedmap.cpp.o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 69%] Built target domdec-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/bitmask32.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/applied_forces-test.dir/densityfitting.cpp.o CMakeFiles/applied_forces-test.dir/densityfittingoptions.cpp.o CMakeFiles/applied_forces-test.dir/densityfittingamplitudelookup.cpp.o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 70%] Built target applied_forces-test /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/ewald/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color= Scanning dependencies of target ewald-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/tests/pmebsplinetest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/leapfrogtestdata.cpp /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fft/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/fft/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color= Scanning dependencies of target fft-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fft-test.dir/fft.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fft/tests/fft.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/tests/pmegathertest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/settle.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fft-test.dir/fft.cpp.o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 70%] Built target fft-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/settletestdata.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/settletestrunners.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/shake.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/simulationsignal.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/tests/pmesolvetest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/bitmask64.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/bitmask128.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/updategroups.cpp /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gpu_utils/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gpu_utils/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color= Scanning dependencies of target gpu_utils-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/gputest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gpu_utils/tests/gputest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/updategroupscog.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/cstringutil.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gpu_utils/tests/clfftinitializer.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/tests/pmesplinespreadtest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/defaultinitializationallocator.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gpu_utils/tests/hostallocator.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/constr.cpp.o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o CMakeFiles/mdlib-test.dir/ebin.cpp.o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o CMakeFiles/mdlib-test.dir/expanded.cpp.o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o CMakeFiles/mdlib-test.dir/settle.cpp.o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o CMakeFiles/mdlib-test.dir/shake.cpp.o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o CMakeFiles/mdlib-test.dir/updategroups.cpp.o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/enumerationhelpers.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 71%] Built target mdlib-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/fixedcapacityvector.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/inmemoryserializer.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/keyvaluetreeserializer.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/tests/pmetestcommon.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/keyvaluetreetransform.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/tests/testhardwarecontexts.cpp /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/hardware/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/hardware/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color= Scanning dependencies of target hardware-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/hardware/tests/hardwaretopology.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/logger.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/logger.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 72%] Built target ewald-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/mutex.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/path.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/path.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 73%] Built target hardware-test /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/math/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color= Scanning dependencies of target math-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/arrayrefwithpadding.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/physicalnodecommunicator.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gpu_utils/tests/devicetransfers.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/stringutil.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/textreader.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gpu_utils-test.dir/gputest.cpp.o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 73%] Built target gpu_utils-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdrunutility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-test-shared make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/coordinatetransformation.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o /usr/bin/ranlib ../../../../lib/libmdrunutility-test-shared.a make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 73%] Built target mdrunutility-test-shared /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdspan/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdspan/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdspan-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdspan/tests/accessor_policy.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/extents.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdspan/tests/extents.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/textwriter.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/densityfit.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/densityfit.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/dofit.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/dofit.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/extensions.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdspan/tests/extensions.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/typetraits.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/exponentialmovingaverage.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-test.dir/alignedallocator.cpp.o CMakeFiles/utility-test.dir/arrayref.cpp.o CMakeFiles/utility-test.dir/bitmask32.cpp.o CMakeFiles/utility-test.dir/bitmask64.cpp.o CMakeFiles/utility-test.dir/bitmask128.cpp.o CMakeFiles/utility-test.dir/cstringutil.cpp.o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/stringutil.cpp.o CMakeFiles/utility-test.dir/textreader.cpp.o CMakeFiles/utility-test.dir/textwriter.cpp.o CMakeFiles/utility-test.dir/typetraits.cpp.o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/layouts.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdspan/tests/layouts.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 74%] Built target utility-test /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/onlinehelp/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/onlinehelp/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color= Scanning dependencies of target onlinehelp-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/onlinehelp/tests/helpformat.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/onlinehelp/tests/helpmanager.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/mdspan.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdspan/tests/mdspan.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/functions.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/functions.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/gausstransform.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/gausstransform.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/onlinehelp/tests/helpwritercontext.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/densityfittingforce.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/invertmatrix.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 75%] Built target onlinehelp-test /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/options/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/options/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color= Scanning dependencies of target options-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/options/tests/abstractoptionstorage.cpp /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/pbcutil/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/pbcutil/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake --color= Scanning dependencies of target pbcutil-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/pbcutil/tests/pbc.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/matrix.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/matrix.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/pbcutil/tests/pbcenums.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pbcutil-test.dir/pbc.cpp.o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 75%] Built target pbcutil-test /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/random/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/random/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color= Scanning dependencies of target random-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/random/tests/exponentialdistribution.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/multidimarray.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o CMakeFiles/mdspan-test.dir/extents.cpp.o CMakeFiles/mdspan-test.dir/extensions.cpp.o CMakeFiles/mdspan-test.dir/layouts.cpp.o CMakeFiles/mdspan-test.dir/mdspan.cpp.o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 76%] Built target mdspan-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/random/tests/gammadistribution.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/random/tests/normaldistribution.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/options/tests/filenameoption.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/seed.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/random/tests/seed.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/paddedvector.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/random/tests/tabulatednormaldistribution.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/threefry.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/random/tests/threefry.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/options/tests/filenameoptionmanager.cpp /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/restraint/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/restraint/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color= Scanning dependencies of target restraintpotential-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/restraint/tests/manager.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/random/tests/uniformintdistribution.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/restraintpotential-test.dir/manager.cpp.o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 76%] Built target restraintpotential-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/option.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/options/tests/option.cpp /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/tables/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/tables/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color= Scanning dependencies of target table-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/options/tests/optionsassigner.cpp make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/tables/tests/splinetable.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/random/tests/uniformrealdistribution.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/random-test.dir/exponentialdistribution.cpp.o CMakeFiles/random-test.dir/gammadistribution.cpp.o CMakeFiles/random-test.dir/normaldistribution.cpp.o CMakeFiles/random-test.dir/seed.cpp.o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o CMakeFiles/random-test.dir/threefry.cpp.o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 77%] Built target random-test /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/taskassignment/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/taskassignment/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color= Scanning dependencies of target taskassignment-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/taskassignment/tests/usergpuids.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/vectypes.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/options/tests/repeatingsection.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o CMakeFiles/math-test.dir/densityfit.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/gausstransform.cpp.o CMakeFiles/math-test.dir/densityfittingforce.cpp.o CMakeFiles/math-test.dir/invertmatrix.cpp.o CMakeFiles/math-test.dir/matrix.cpp.o CMakeFiles/math-test.dir/multidimarray.cpp.o CMakeFiles/math-test.dir/paddedvector.cpp.o CMakeFiles/math-test.dir/vectypes.cpp.o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 77%] Built target taskassignment-test /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/topology/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/topology/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake --color= Scanning dependencies of target topology-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/topology/tests/exclusionblocks.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 79%] Built target math-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/topology/tests/mtop.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/table-test.dir/splinetable.cpp.o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 79%] Built target table-test /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/pulling/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/pulling/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color= Scanning dependencies of target pull-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pull-test.dir/pull.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/pulling/tests/pull.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/topology/tests/symtab.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/options/tests/timeunitmanager.cpp /usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/awh/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/awh/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color= Scanning dependencies of target awh-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/bias.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/awh/tests/bias.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pull-test.dir/pull.cpp.o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 79%] Built target pull-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/awh/tests/biasstate.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/topology-test.dir/exclusionblocks.cpp.o CMakeFiles/topology-test.dir/mtop.cpp.o CMakeFiles/topology-test.dir/symtab.cpp.o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 79%] Built target topology-test /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/simd/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color= Scanning dependencies of target simd-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/bootstrap_loadstore.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/options/tests/treesupport.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/grid.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/awh/tests/grid.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/base.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/base.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/compat/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/compat/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color= Scanning dependencies of target compat-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-unused-member-function -o CMakeFiles/compat-test.dir/optional.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/compat/tests/optional.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/grid.cpp.o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/awh-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 79%] Built target awh-test /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxana/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake --color= Scanning dependencies of target gmxana-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxana/tests/entropy.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxana/tests/gmx_traj.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd_floatingpoint.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxana/tests/gmx_mindist.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o CMakeFiles/options-test.dir/filenameoption.cpp.o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o CMakeFiles/options-test.dir/option.cpp.o CMakeFiles/options-test.dir/optionsassigner.cpp.o CMakeFiles/options-test.dir/repeatingsection.cpp.o CMakeFiles/options-test.dir/timeunitmanager.cpp.o CMakeFiles/options-test.dir/treesupport.cpp.o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 80%] Built target options-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake --color= Scanning dependencies of target pdb2gmx3-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxana/tests/gmx_msd.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd_floatingpoint_util.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxana-test.dir/entropy.cpp.o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 81%] Built target gmxana-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/compat/tests/pointers.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd_vector_operations.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx3-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 82%] Built target pdb2gmx3-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake --color= Scanning dependencies of target pdb2gmx2-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake --color= Scanning dependencies of target pdb2gmx1-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd_math.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/string_view.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/compat/tests/string_view.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx2-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 82%] Built target pdb2gmx2-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 82%] Built target pdb2gmx1-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake --color= Scanning dependencies of target gmxpreprocess-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/editconf.cpp /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/correlationfunctions/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/correlationfunctions/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake --color= Scanning dependencies of target correlations-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/autocorr.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/correlationfunctions/tests/autocorr.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd_memory.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/correlationfunctions/tests/correlationdataset.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/expfit.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/correlationfunctions/tests/expfit.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/compat-test.dir/optional.cpp.o CMakeFiles/compat-test.dir/pointers.cpp.o CMakeFiles/compat-test.dir/string_view.cpp.o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/genconf.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 82%] Built target compat-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/analysisdata/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/analysisdata/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake --color= Scanning dependencies of target analysisdata-test-shared make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/analysisdata/tests/datatest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/genion.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/correlations-test.dir/autocorr.cpp.o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o CMakeFiles/correlations-test.dir/expfit.cpp.o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 83%] Built target correlations-test /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/coordinateio/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/DependInfo.cmake --color= Scanning dependencies of target coordinateio-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/builder.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/coordinateio/tests/builder.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/genrestr.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd_integer.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/analysisdata/tests/mock_datamodule.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/coordinateio/tests/outputadaptercontainer.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd4.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/coordinateio/tests/outputadapters.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd4_floatingpoint.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/insert_molecules.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/readir.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd4_vector_operations.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libanalysisdata-test-shared.a CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o /usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 83%] Built target analysisdata-test-shared /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/energyanalysis/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/energyanalysis/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake --color= Scanning dependencies of target energyanalysis-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/energyanalysis/tests/legacyenergy.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd4_math.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/solvate.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/scalar.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 83%] Built target energyanalysis-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/scalar_util.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/topdirs.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/requirements.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/coordinateio/tests/requirements.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 84%] Built target gmxpreprocess-test /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/tools/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/tools/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake --color= Scanning dependencies of target tool-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/dump.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/tools/tests/dump.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/scalar_math.cpp /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/fileio/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color= Scanning dependencies of target fileio-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio/tests/confio.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/tools/tests/report_methods.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/coordinateio/tests/setatoms.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio/tests/filemd5.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/trjconv.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/tools/tests/trjconv.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/base.cpp.o CMakeFiles/simd-test.dir/simd.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4_math.cpp.o CMakeFiles/simd-test.dir/scalar.cpp.o CMakeFiles/simd-test.dir/scalar_util.cpp.o CMakeFiles/simd-test.dir/scalar_math.cpp.o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/coordinateio/tests/setbothtime.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 86%] Built target simd-test /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/selection/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake --color= Scanning dependencies of target selection-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/tests/indexutil.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio/tests/mrcserializer.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/coordinateio/tests/setstarttime.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio/tests/mrcdensitymap.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/tool-test.dir/dump.cpp.o CMakeFiles/tool-test.dir/report_methods.cpp.o CMakeFiles/tool-test.dir/trjconv.cpp.o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 87%] Built target tool-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun-modules-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/densityfittingmodule.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/coordinateio/tests/settimestep.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/tests/nbsearch.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/coordinateio/tests/testmodule.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/interactiveMD.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio/tests/mrcdensitymapheader.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/coordinateio-test.dir/builder.cpp.o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o CMakeFiles/coordinateio-test.dir/requirements.cpp.o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 88%] Built target coordinateio-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun-tpi-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/tpitest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/mimic.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio/tests/readinp.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/tests/poscalc.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio/tests/fileioxdrserializer.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-modules-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 88%] Built target mdrun-modules-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio/tests/tngio.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-tpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 89%] Built target mdrun-tpi-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/tests/selectioncollection.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/dispersion_correction.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/dispersion_correction.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/tests/selectionoption.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 90%] Built target fileio-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/tests/toputils.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/orires.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/orires.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/pmetest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/pmetest.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun-output-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/compressed_x_output.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/simulator.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/simulator.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/helpwriting.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/outputfiles.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/trajectory_writing.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/swapcoords.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 91%] Built target mdrun-output-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun-non-integrator-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/minimize.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/selection-test.dir/indexutil.cpp.o CMakeFiles/selection-test.dir/nbsearch.cpp.o CMakeFiles/selection-test.dir/poscalc.cpp.o CMakeFiles/selection-test.dir/selectioncollection.cpp.o CMakeFiles/selection-test.dir/selectionoption.cpp.o CMakeFiles/selection-test.dir/toputils.cpp.o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun-mpi-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/domain_decomposition.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 91%] Built target selection-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun-io-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/exactcontinuation.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-test.dir/dispersion_correction.cpp.o CMakeFiles/mdrun-test.dir/orires.cpp.o CMakeFiles/mdrun-test.dir/pmetest.cpp.o CMakeFiles/mdrun-test.dir/simulator.cpp.o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 91%] Built target mdrun-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/minimize.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/nonbonded_bench.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/normalmodes.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/mimic.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/rerun.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/grompp.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/initialconstraints.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/termination.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/termination.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/multisim.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/multisimtest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/simple_mdrun.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-io-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o CMakeFiles/mdrun-io-test.dir/termination.cpp.o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-io-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun-mpi-coordination-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/periodicactions.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 92%] Built target mdrun-io-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/pmetest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp /usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target gmxapi-mpi-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests/restraint.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/replicaexchange.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 92%] Built target mdrun-non-integrator-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests/status.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests/system.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests/version.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-coordination-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-coordination-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread /usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/DependInfo.cmake --color= Scanning dependencies of target gmxapi-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/restraint.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests/restraint.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 93%] Built target mdrun-mpi-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/status.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests/status.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 93%] Built target mdrun-mpi-coordination-test /usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/workflow/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/workflow/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target workflow-details-mpi-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/workflow/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-mpi-test.dir/workflow.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/workflow/tests/workflow.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests/runner.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/system.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests/system.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests/stopsignaler.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/version.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests/version.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/workflow/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-mpi-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/runner.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests/runner.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/workflow-details-mpi-test.dir/workflow.cpp.o CMakeFiles/workflow-details-mpi-test.dir/__/__/__/__/testutils/unittest_main.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-mpi-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi.so.0.1.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../../lib/libgmock.so ../../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 93%] Built target workflow-details-mpi-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests/stopsignaler.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o CMakeFiles/gmxapi-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi.so.0.1.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread /usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/workflow/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/workflow/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/DependInfo.cmake --color= Scanning dependencies of target workflow-details-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/workflow/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-test.dir/workflow.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/workflow/tests/workflow.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 93%] Built target gmxapi-mpi-test /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/commandline/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color= Scanning dependencies of target commandline-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdrunutility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-mpi-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/workflow/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxapi-test.dir/restraint.cpp.o CMakeFiles/gmxapi-test.dir/status.cpp.o CMakeFiles/gmxapi-test.dir/system.cpp.o CMakeFiles/gmxapi-test.dir/version.cpp.o CMakeFiles/gmxapi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/gmxapi-test.dir/runner.cpp.o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi.so.0.1.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 94%] Built target gmxapi-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external 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CMakeFiles/workflow-details-test.dir/__/__/__/__/testutils/unittest_main.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi.so.0.1.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../../lib/libgmock.so ../../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 95%] Built target workflow-details-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdrunutility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdrunutility/tests/threadaffinity.cpp /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/analysisdata/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/analysisdata/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake --color= Scanning dependencies of target analysisdata-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/analysisdata/tests/analysisdata.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 96%] Built target mdrunutility-mpi-test /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake --color= Scanning dependencies of target trajectoryanalysis-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/moduletest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 96%] Built target mdrunutility-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. 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/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/freevolume.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/pairdist.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o CMakeFiles/analysisdata-test.dir/average.cpp.o CMakeFiles/analysisdata-test.dir/histogram.cpp.o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/rdf.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 96%] Built target analysisdata-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/sasa.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/select.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o CMakeFiles/commandline-test.dir/filenm.cpp.o CMakeFiles/commandline-test.dir/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 97%] Built target commandline-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/trajectory.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/unionfind.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [100%] Built target trajectoryanalysis-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/CMakeFiles/tests.dir/DependInfo.cmake --color= Scanning dependencies of target tests make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [100%] Built target tests make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/cmake -E cmake_progress_start /build/gromacs-5atmZb/gromacs-2020.6/build/basic/CMakeFiles 0 make[2]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' make[1]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' (cd build/basic; LD_LIBRARY_PATH=/build/gromacs-5atmZb/gromacs-2020.6/build/basic/lib ctest -V || dpkg-architecture -i hurd-i386 ) UpdateCTestConfiguration from :/build/gromacs-5atmZb/gromacs-2020.6/build/basic/DartConfiguration.tcl Parse Config file:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/DartConfiguration.tcl UpdateCTestConfiguration from :/build/gromacs-5atmZb/gromacs-2020.6/build/basic/DartConfiguration.tcl Parse Config file:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/DartConfiguration.tcl Test project /build/gromacs-5atmZb/gromacs-2020.6/build/basic Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: TestUtilsUnitTests 1: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/testutils-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/TestUtilsUnitTests.xml" 1: Test timeout computed to be: 30 1: [==========] Running 59 tests from 5 test cases. 1: [----------] Global test environment set-up. 1: [----------] 10 tests from InteractiveTestHelperTest 1: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 1: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (40 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (1 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 1: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (4 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 1: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 1: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) 1: [----------] 10 tests from InteractiveTestHelperTest (48 ms total) 1: 1: [----------] 34 tests from ReferenceDataTest 1: [ RUN ] ReferenceDataTest.HandlesSimpleData 1: [ OK ] ReferenceDataTest.HandlesSimpleData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 1: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 1: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesStringBlockData 1: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesVectorData 1: [ OK ] ReferenceDataTest.HandlesVectorData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceData 1: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 1: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesIncorrectData 1: [ OK ] ReferenceDataTest.HandlesIncorrectData (7 ms) 1: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 1: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMissingData 1: [ OK ] ReferenceDataTest.HandlesMissingData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedData 1: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesAnys 1: [ OK ] ReferenceDataTest.HandlesAnys (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 1: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue 1: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType 1: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 1: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 1: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 1: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 1: [ OK ] ReferenceDataTest.HandlesEmptyStrings (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 1: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 1: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 1: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 1: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 1: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesReadingValues 1: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (0 ms) 1: [----------] 34 tests from ReferenceDataTest (17 ms total) 1: 1: [----------] 7 tests from FloatingPointDifferenceTest 1: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 1: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 1: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 1: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 1: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 1: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 1: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 1: 1: [----------] 4 tests from FloatingPointToleranceTest 1: [ RUN ] FloatingPointToleranceTest.UlpTolerance 1: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 1: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 1: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 1: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 1: 1: [----------] 4 tests from XvgTests 1: [ RUN ] XvgTests.CreateFile 1: [ OK ] XvgTests.CreateFile (1 ms) 1: [ RUN ] XvgTests.CheckMissing 1: [ OK ] XvgTests.CheckMissing (0 ms) 1: [ RUN ] XvgTests.CheckExtra 1: [ OK ] XvgTests.CheckExtra (0 ms) 1: [ RUN ] XvgTests.ReadIncorrect 1: [ OK ] XvgTests.ReadIncorrect (0 ms) 1: [----------] 4 tests from XvgTests (2 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 59 tests from 5 test cases ran. (67 ms total) 1: [ PASSED ] 59 tests. 1/54 Test #1: TestUtilsUnitTests .................. Passed 0.19 sec test 2 Start 2: TestUtilsMpiUnitTests 2: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/TestUtilsMpiUnitTests.xml" 2: Test timeout computed to be: 30 2: [==========] Running 1 test from 1 test case. 2: [----------] Global test environment set-up. 2: [----------] 1 test from MpiSelfTest 2: [ RUN ] MpiSelfTest.Runs 2: [ OK ] MpiSelfTest.Runs (0 ms) 2: [----------] 1 test from MpiSelfTest (0 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 1 test from 1 test case ran. (0 ms total) 2: [ PASSED ] 1 test. 2/54 Test #2: TestUtilsMpiUnitTests ............... Passed 0.02 sec test 3 Start 3: UtilityUnitTests 3: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/utility-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/UtilityUnitTests.xml" 3: Test timeout computed to be: 30 3: [==========] Running 347 tests from 56 test cases. 3: [----------] Global test environment set-up. 3: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 3: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/0.Move 3: [ OK ] AllocatorTest/0.Move (0 ms) 3: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/0 (0 ms total) 3: 3: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 3: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (1 ms) 3: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/1.Move 3: [ OK ] AllocatorTest/1.Move (0 ms) 3: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/1 (1 ms total) 3: 3: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 3: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/2.Move 3: [ OK ] AllocatorTest/2.Move (0 ms) 3: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/2 (0 ms total) 3: 3: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 3: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/3.Move 3: [ OK ] AllocatorTest/3.Move (0 ms) 3: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/3 (0 ms total) 3: 3: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 3: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/4.Move 3: [ OK ] AllocatorTest/4.Move (0 ms) 3: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/4 (0 ms total) 3: 3: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 3: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (1 ms) 3: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/5.Move 3: [ OK ] AllocatorTest/5.Move (0 ms) 3: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/5 (1 ms total) 3: 3: [----------] 1 test from AllocatorUntypedTest 3: [ RUN ] AllocatorUntypedTest.Comparison 3: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 3: [----------] 1 test from AllocatorUntypedTest (0 ms total) 3: 3: [----------] 1 test from EmptyArrayRefTest 3: [ RUN ] EmptyArrayRefTest.IsEmpty 3: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 3: [----------] 1 test from EmptyArrayRefTest (0 ms total) 3: 3: [----------] 1 test from EmptyConstArrayRefTest 3: [ RUN ] EmptyConstArrayRefTest.IsEmpty 3: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 3: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/1 (1 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/9 (1 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/18 (1 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 3: 3: [----------] 2 tests from CStringUtilityTest 3: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison 3: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) 3: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength 3: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms) 3: [----------] 2 tests from CStringUtilityTest (0 ms total) 3: 3: [----------] 2 tests from DefaultInitializationAllocator 3: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization 3: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) 3: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization 3: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) 3: [----------] 2 tests from DefaultInitializationAllocator (0 ms total) 3: 3: [----------] 4 tests from EnumerationHelpersTest 3: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks 3: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms) 3: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks 3: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) 3: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe 3: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) 3: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks 3: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) 3: [----------] 4 tests from EnumerationHelpersTest (0 ms total) 3: 3: [----------] 9 tests from FixedCapacityVectorTest 3: [ RUN ] FixedCapacityVectorTest.IsEmpty 3: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) 3: [ RUN ] FixedCapacityVectorTest.PushWorks 3: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.PopWorks 3: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.ClearWorks 3: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks 3: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.AtThrows 3: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms) 3: [ RUN ] FixedCapacityVectorTest.IteratorWorks 3: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks 3: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks 3: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) 3: [----------] 9 tests from FixedCapacityVectorTest (0 ms total) 3: 3: [----------] 5 tests from InMemorySerializerTest 3: [ RUN ] InMemorySerializerTest.Roundtrip 3: [ OK ] InMemorySerializerTest.Roundtrip (0 ms) 3: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap 3: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) 3: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap 3: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) 3: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap 3: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms) 3: [ RUN ] InMemorySerializerTest.SizeIsCorrect 3: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) 3: [----------] 5 tests from InMemorySerializerTest (0 ms total) 3: 3: [----------] 4 tests from KeyValueTreeSerializerTest 3: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 3: [ OK ] KeyValueTreeSerializerTest.EmptyTree (1 ms) 3: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 3: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) 3: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 3: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms) 3: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 3: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) 3: [----------] 4 tests from KeyValueTreeSerializerTest (1 ms total) 3: 3: [----------] 6 tests from TreeValueTransformTest 3: [ RUN ] TreeValueTransformTest.SimpleTransforms 3: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) 3: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 3: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) 3: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 3: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (1 ms) 3: [ RUN ] TreeValueTransformTest.ObjectFromString 3: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) 3: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 3: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) 3: [ RUN ] TreeValueTransformTest.ScopedTransformRules 3: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 3: [----------] 6 tests from TreeValueTransformTest (1 ms total) 3: 3: [----------] 1 test from TreeValueTransformErrorTest 3: [ RUN ] TreeValueTransformErrorTest.ConversionError 3: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms) 3: [----------] 1 test from TreeValueTransformErrorTest (0 ms total) 3: 3: [----------] 7 tests from LoggerTest 3: [ RUN ] LoggerTest.EmptyLoggerWorks 3: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 3: [ RUN ] LoggerTest.LogsToStream 3: [ OK ] LoggerTest.LogsToStream (0 ms) 3: [ RUN ] LoggerTest.LogsToFile 3: [ OK ] LoggerTest.LogsToFile (8 ms) 3: [ RUN ] LoggerTest.LevelFilteringWorks 3: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 3: [ RUN ] LoggerTest.LogsToMultipleStreams 3: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 3: [ RUN ] LoggerTest.LogsToMultipleFiles 3: [ OK ] LoggerTest.LogsToMultipleFiles (1 ms) 3: [ RUN ] LoggerTest.LogsToStreamAndFile 3: [ OK ] LoggerTest.LogsToStreamAndFile (0 ms) 3: [----------] 7 tests from LoggerTest (9 ms total) 3: 3: [----------] 4 tests from MutexBasicTest 3: [ RUN ] MutexBasicTest.CanBeMade 3: [ OK ] MutexBasicTest.CanBeMade (0 ms) 3: [ RUN ] MutexBasicTest.CanBeLocked 3: [ OK ] MutexBasicTest.CanBeLocked (0 ms) 3: [ RUN ] MutexBasicTest.CanBeTryLocked 3: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms) 3: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard 3: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms) 3: [----------] 4 tests from MutexBasicTest (0 ms total) 3: 3: [----------] 3 tests from MutexTaskTest 3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock 3: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (1 ms) 3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread 3: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (0 ms) 3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread 3: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms) 3: [----------] 3 tests from MutexTaskTest (1 ms total) 3: 3: [----------] 2 tests from PathTest 3: [ RUN ] PathTest.StripSourcePrefixWorks 3: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 3: [ RUN ] PathTest.SearchOperationsWork 3: [ OK ] PathTest.SearchOperationsWork (0 ms) 3: [----------] 2 tests from PathTest (0 ms total) 3: 3: [----------] 2 tests from PhysicalNodeCommunicatorTest 3: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 3: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 3: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 3: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 3: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 3: 3: [----------] 9 tests from StringUtilityTest 3: [ RUN ] StringUtilityTest.StartsWith 3: [ OK ] StringUtilityTest.StartsWith (0 ms) 3: [ RUN ] StringUtilityTest.EndsWith 3: [ OK ] StringUtilityTest.EndsWith (0 ms) 3: [ RUN ] StringUtilityTest.StripSuffixIfPresent 3: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 3: [ RUN ] StringUtilityTest.StripString 3: [ OK ] StringUtilityTest.StripString (0 ms) 3: [ RUN ] StringUtilityTest.SplitString 3: [ OK ] StringUtilityTest.SplitString (0 ms) 3: [ RUN ] StringUtilityTest.SplitDelimitedString 3: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 3: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 3: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) 3: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive 3: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) 3: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength 3: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) 3: [----------] 9 tests from StringUtilityTest (1 ms total) 3: 3: [----------] 2 tests from FormatStringTest 3: [ RUN ] FormatStringTest.HandlesBasicFormatting 3: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 3: [ RUN ] FormatStringTest.HandlesLongStrings 3: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 3: [----------] 2 tests from FormatStringTest (0 ms total) 3: 3: [----------] 1 test from StringFormatterTest 3: [ RUN ] StringFormatterTest.HandlesBasicFormatting 3: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 3: [----------] 1 test from StringFormatterTest (0 ms total) 3: 3: [----------] 1 test from formatAndJoinTest 3: [ RUN ] formatAndJoinTest.Works 3: [ OK ] formatAndJoinTest.Works (0 ms) 3: [----------] 1 test from formatAndJoinTest (0 ms total) 3: 3: [----------] 1 test from JoinStringsTest 3: [ RUN ] JoinStringsTest.Works 3: [ OK ] JoinStringsTest.Works (0 ms) 3: [----------] 1 test from JoinStringsTest (0 ms total) 3: 3: [----------] 6 tests from ReplaceAllTest 3: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 3: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesNoMatches 3: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 3: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 3: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 3: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 3: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 3: [----------] 6 tests from ReplaceAllTest (0 ms total) 3: 3: [----------] 10 tests from TextLineWrapperTest 3: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 3: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 3: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 3: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 3: [ RUN ] TextLineWrapperTest.WrapsCorrectly 3: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms) 3: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 3: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesIndent 3: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 3: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 3: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 3: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) 3: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 3: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (1 ms) 3: [----------] 10 tests from TextLineWrapperTest (1 ms total) 3: 3: [----------] 6 tests from TextWriterTest 3: [ RUN ] TextWriterTest.WritesLines 3: [ OK ] TextWriterTest.WritesLines (0 ms) 3: [ RUN ] TextWriterTest.WritesLinesInParts 3: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 3: [ RUN ] TextWriterTest.WritesWrappedLines 3: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) 3: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 3: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 3: [ RUN ] TextWriterTest.TracksNewlines 3: [ OK ] TextWriterTest.TracksNewlines (0 ms) 3: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 3: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 3: [----------] 6 tests from TextWriterTest (0 ms total) 3: 3: [----------] 1 test from TypeTraitsTest 3: [ RUN ] TypeTraitsTest.IsIntegralConstant 3: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 3: [----------] 1 test from TypeTraitsTest (0 ms total) 3: 3: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 3: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 3: 3: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 3: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 3: 3: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 3: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 3: 3: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (1 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms) 3: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (1 ms total) 3: 3: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 3: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (0 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 347 tests from 56 test cases ran. (20 ms total) 3: [ PASSED ] 347 tests. 3/54 Test #3: UtilityUnitTests .................... Passed 0.20 sec test 4 Start 4: UtilityMpiUnitTests 4: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/utility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/UtilityMpiUnitTests.xml" 4: Test timeout computed to be: 30 4: [==========] Running 2 tests from 1 test case. 4: [----------] Global test environment set-up. 4: [----------] 2 tests from PhysicalNodeCommunicatorTest 4: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 4: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 4: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 4: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (1 ms) 4: [----------] 2 tests from PhysicalNodeCommunicatorTest (1 ms total) 4: 4: [----------] Global test environment tear-down 4: [==========] 2 tests from 1 test case ran. (1 ms total) 4: [ PASSED ] 2 tests. 4/54 Test #4: UtilityMpiUnitTests ................. Passed 0.01 sec test 5 Start 5: MdlibUnitTest 5: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/mdlib-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/MdlibUnitTest.xml" 5: Test timeout computed to be: 30 5: [==========] Running 187 tests from 13 test cases. 5: [----------] Global test environment set-up. 5: [----------] 1 test from VerletBufferConstraintTest 5: [ RUN ] VerletBufferConstraintTest.EqualMasses 5: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 5: [----------] 1 test from VerletBufferConstraintTest (0 ms total) 5: 5: [----------] 2 tests from PrEbinTest 5: [ RUN ] PrEbinTest.HandlesAverages 5: [ OK ] PrEbinTest.HandlesAverages (0 ms) 5: [ RUN ] PrEbinTest.HandlesEmptyAverages 5: [ OK ] PrEbinTest.HandlesEmptyAverages (0 ms) 5: [----------] 2 tests from PrEbinTest (0 ms total) 5: 5: [----------] 4 tests from ShakeTest 5: [ RUN ] ShakeTest.ConstrainsOneBond 5: [ OK ] ShakeTest.ConstrainsOneBond (1 ms) 5: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 5: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 5: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 5: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 5: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 5: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 5: [----------] 4 tests from ShakeTest (1 ms total) 5: 5: [----------] 1 test from NullSignalTest 5: [ RUN ] NullSignalTest.NullSignallerWorks 5: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 5: [----------] 1 test from NullSignalTest (0 ms total) 5: 5: [----------] 7 tests from SignalTest 5: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 5: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 5: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 5: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 5: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 5: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 5: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 5: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 5: [----------] 7 tests from SignalTest (0 ms total) 5: 5: [----------] 9 tests from UpdateGroups 5: [ RUN ] UpdateGroups.ethaneUA 5: [ OK ] UpdateGroups.ethaneUA (0 ms) 5: [ RUN ] UpdateGroups.methane 5: [ OK ] UpdateGroups.methane (0 ms) 5: [ RUN ] UpdateGroups.ethane 5: [ OK ] UpdateGroups.ethane (0 ms) 5: [ RUN ] UpdateGroups.butaneUA 5: [ OK ] UpdateGroups.butaneUA (0 ms) 5: [ RUN ] UpdateGroups.waterThreeSite 5: [ OK ] UpdateGroups.waterThreeSite (0 ms) 5: [ RUN ] UpdateGroups.waterFourSite 5: [ OK ] UpdateGroups.waterFourSite (0 ms) 5: [ RUN ] UpdateGroups.fourAtomsWithSettle 5: [ OK ] UpdateGroups.fourAtomsWithSettle (0 ms) 5: [ RUN ] UpdateGroups.waterFlexAngle 5: [ OK ] UpdateGroups.waterFlexAngle (0 ms) 5: [ RUN ] UpdateGroups.twoMoltypes 5: [ OK ] UpdateGroups.twoMoltypes (0 ms) 5: [----------] 9 tests from UpdateGroups (0 ms total) 5: 5: [----------] 1 test from UpdateGroupsCog 5: [ RUN ] UpdateGroupsCog.ComputesCogs 5: [ OK ] UpdateGroupsCog.ComputesCogs (1 ms) 5: [----------] 1 test from UpdateGroupsCog (1 ms total) 5: 5: [----------] 84 tests from WithParameters/ConstraintsTest 5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/0 5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/1 5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/2 5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/3 5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/2 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/3 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/4 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/5 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/6 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/7 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/2 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/3 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/4 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/5 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/6 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/7 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/7 (1 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/8 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/8 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/9 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/9 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/10 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/10 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/11 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/11 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/2 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/3 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/4 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/5 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/6 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/7 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/8 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/8 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/9 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/9 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/10 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/10 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/11 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/11 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/12 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/12 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/13 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/13 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/14 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/14 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/15 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/15 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/0 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/1 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/2 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/3 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/3 (1 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/4 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/5 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/6 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/7 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/8 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/8 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/9 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/9 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/10 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/10 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/11 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/11 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/12 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/12 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/13 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/13 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/14 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/14 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/15 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/15 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/16 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/16 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/17 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/17 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/18 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/18 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/19 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/19 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/0 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/1 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/2 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/3 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/4 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/5 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/6 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/7 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/8 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/8 (1 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/9 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/9 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/10 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/10 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/11 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/11 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/12 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/12 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/13 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/13 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/14 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/14 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/15 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/15 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/16 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/16 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/17 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/17 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/18 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/18 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/19 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/19 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/20 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/20 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/21 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/21 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/22 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/22 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/23 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/23 (0 ms) 5: [----------] 84 tests from WithParameters/ConstraintsTest (3 ms total) 5: 5: [----------] 11 tests from WithParameters/EnergyOutputTest 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (3 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (1 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (2 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3 5: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (0 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as single precision energy file 5: Reading energy frame 0 time 10.100 Reading energy frame 1 time 27.500 Reading energy frame 2 time 44.900 Reading energy frame 3 time 62.300 Reading energy frame 4 time 79.700 Reading energy frame 5 time 97.100 Reading energy frame 6 time 114.500 Reading energy frame 7 time 131.900 Reading energy frame 8 time 149.300 Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (6 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (2 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (1 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (3 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (4 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (4 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (16 ms) 5: [----------] 11 tests from WithParameters/EnergyOutputTest (44 ms total) 5: 5: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms) 5: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (0 ms total) 5: 5: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms) 5: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (1 ms total) 5: 5: [----------] 16 tests from WithParameters/LeapFrogTest 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (1 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (2 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (6 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (2 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (2 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (2 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (2 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (2 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (2 ms) 5: [----------] 16 tests from WithParameters/LeapFrogTest (28 ms total) 5: 5: [----------] 13 tests from WithParameters/SettleTest 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (1 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (1 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (1 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (1 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (1 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (1 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (1 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (2 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (1 ms) 5: [----------] 13 tests from WithParameters/SettleTest (11 ms total) 5: 5: [----------] Global test environment tear-down 5: [==========] 187 tests from 13 test cases ran. (89 ms total) 5: [ PASSED ] 187 tests. 5/54 Test #5: MdlibUnitTest ....................... Passed 0.11 sec test 6 Start 6: AppliedForcesUnitTest 6: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/applied_forces-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/AppliedForcesUnitTest.xml" 6: Test timeout computed to be: 30 6: [==========] Running 20 tests from 4 test cases. 6: [----------] Global test environment set-up. 6: [----------] 2 tests from DensityFittingTest 6: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows 6: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (0 ms) 6: [ RUN ] DensityFittingTest.SingleAtom 6: [ OK ] DensityFittingTest.SingleAtom (1 ms) 6: [----------] 2 tests from DensityFittingTest (1 ms total) 6: 6: [----------] 8 tests from DensityFittingOptionsTest 6: [ RUN ] DensityFittingOptionsTest.DefaultParameters 6: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) 6: [ RUN ] DensityFittingOptionsTest.OptionSetsActive 6: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms) 6: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive 6: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 6: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive 6: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (0 ms) 6: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup 6: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 6: [ RUN ] DensityFittingOptionsTest.InternalsToKvt 6: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) 6: [ RUN ] DensityFittingOptionsTest.KvtToInternal 6: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms) 6: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent 6: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms) 6: [----------] 8 tests from DensityFittingOptionsTest (0 ms total) 6: 6: [----------] 7 tests from DensityFittingAmplitudeLookupTest 6: [ RUN ] DensityFittingAmplitudeLookupTest.Unity 6: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.Charge 6: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.Masses 6: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign 6: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct 6: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign 6: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct 6: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) 6: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total) 6: 6: [----------] 3 tests from ElectricFieldTest 6: [ RUN ] ElectricFieldTest.Static 6: [ OK ] ElectricFieldTest.Static (0 ms) 6: [ RUN ] ElectricFieldTest.Oscillating 6: [ OK ] ElectricFieldTest.Oscillating (0 ms) 6: [ RUN ] ElectricFieldTest.Pulsed 6: [ OK ] ElectricFieldTest.Pulsed (0 ms) 6: [----------] 3 tests from ElectricFieldTest (0 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 20 tests from 4 test cases ran. (1 ms total) 6: [ PASSED ] 20 tests. 6/54 Test #6: AppliedForcesUnitTest ............... Passed 0.01 sec test 7 Start 7: CommandLineUnitTests 7: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/commandline-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/CommandLineUnitTests.xml" 7: Test timeout computed to be: 30 7: [==========] Running 59 tests from 7 test cases. 7: [----------] Global test environment set-up. 7: [----------] 3 tests from CommandLineHelpModuleTest 7: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 7: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (0 ms) 7: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 7: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (1 ms) 7: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 7: [ OK ] CommandLineHelpModuleTest.ExportsHelp (0 ms) 7: [----------] 3 tests from CommandLineHelpModuleTest (1 ms total) 7: 7: [----------] 7 tests from CommandLineHelpWriterTest 7: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 7: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (1 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 7: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 7: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 7: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 7: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 7: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (1 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues 7: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms) 7: [----------] 7 tests from CommandLineHelpWriterTest (2 ms total) 7: 7: [----------] 6 tests from CommandLineModuleManagerTest 7: [ RUN ] CommandLineModuleManagerTest.RunsModule 7: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) 7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 7: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 7: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 7: [----------] 6 tests from CommandLineModuleManagerTest (0 ms total) 7: 7: [----------] 13 tests from CommandLineParserTest 7: [ RUN ] CommandLineParserTest.HandlesSingleValues 7: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 7: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 7: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 7: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 7: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 7: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesString 7: [ OK ] CommandLineParserTest.HandlesString (0 ms) 7: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 7: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 7: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 7: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 7: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 7: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 7: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 7: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 7: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 7: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 7: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 7: [----------] 13 tests from CommandLineParserTest (1 ms total) 7: 7: [----------] 6 tests from CommandLineProgramContextTest 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 7: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 7: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 7: [----------] 6 tests from CommandLineProgramContextTest (0 ms total) 7: 7: [----------] 3 tests from OutputNamesTest 7: [ RUN ] OutputNamesTest.CanBeSuffixed 7: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) 7: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend 7: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) 7: [ RUN ] OutputNamesTest.CanHavePartNumberAdded 7: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms) 7: [----------] 3 tests from OutputNamesTest (0 ms total) 7: 7: [----------] 21 tests from ParseCommonArgsTest 7: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 7: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 7: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 7: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 7: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 7: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 7: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 7: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 7: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 7: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 7: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 7: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 7: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 7: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 7: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 7: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 7: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 7: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (1 ms) 7: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 7: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 7: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 7: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (0 ms) 7: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 7: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 7: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 7: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (1 ms) 7: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 7: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (21 ms) 7: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 7: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 7: [----------] 21 tests from ParseCommonArgsTest (23 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 59 tests from 7 test cases ran. (27 ms total) 7: [ PASSED ] 59 tests. 7/54 Test #7: CommandLineUnitTests ................ Passed 0.04 sec test 8 Start 8: DomDecTests 8: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/domdec-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/DomDecTests.xml" 8: Test timeout computed to be: 30 8: [==========] Running 9 tests from 2 test cases. 8: [----------] Global test environment set-up. 8: [----------] 7 tests from HashedMap 8: [ RUN ] HashedMap.InsertsFinds 8: [ OK ] HashedMap.InsertsFinds (0 ms) 8: [ RUN ] HashedMap.NegativeKeysWork 8: [ OK ] HashedMap.NegativeKeysWork (0 ms) 8: [ RUN ] HashedMap.InsertsErases 8: [ OK ] HashedMap.InsertsErases (0 ms) 8: [ RUN ] HashedMap.InsertsOrAssigns 8: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 8: [ RUN ] HashedMap.Clears 8: [ OK ] HashedMap.Clears (0 ms) 8: [ RUN ] HashedMap.LinkedEntries 8: [ OK ] HashedMap.LinkedEntries (0 ms) 8: [ RUN ] HashedMap.ResizesTable 8: [ OK ] HashedMap.ResizesTable (0 ms) 8: [----------] 7 tests from HashedMap (0 ms total) 8: 8: [----------] 2 tests from LocalAtomSetManager 8: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 8: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 8: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 8: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 8: [----------] 2 tests from LocalAtomSetManager (0 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 9 tests from 2 test cases ran. (0 ms total) 8: [ PASSED ] 9 tests. 8/54 Test #8: DomDecTests ......................... Passed 0.02 sec test 9 Start 9: EwaldUnitTests 9: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/ewald-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/EwaldUnitTests.xml" 9: Test timeout computed to be: 30 9: [==========] Running 257 tests from 10 test cases. 9: [----------] Global test environment set-up. 9: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (2 ms) 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 9: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (3 ms total) 9: 9: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (0 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (5 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (52 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (3 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (3 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (4 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (3 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (3 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (2 ms) 9: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (95 ms total) 9: 9: [----------] 144 tests from SaneInput/PmeGatherTest 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/72 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/72 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/73 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/73 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/74 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/74 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/75 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/75 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/76 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/76 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/77 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/77 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/78 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/78 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/79 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/79 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/80 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/80 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/81 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/81 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/82 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/82 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/83 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/83 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/84 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/84 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/85 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/85 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/86 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/86 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/87 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/87 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/88 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/88 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/89 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/89 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/90 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/90 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/91 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/91 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/92 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/92 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/93 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/93 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/94 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/94 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/95 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/95 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/96 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/96 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/97 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/97 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/98 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/98 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/99 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/99 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/100 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/100 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/101 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/101 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/102 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/102 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/103 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/103 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/104 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/104 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/105 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/105 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/106 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/106 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/107 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/107 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/108 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/108 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/109 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/109 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/110 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/110 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/111 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/111 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/112 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/112 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/113 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/113 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/114 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/114 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/115 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/115 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/116 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/116 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/117 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/117 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/118 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/118 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/119 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/119 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/120 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/120 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/121 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/121 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/122 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/122 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/123 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/123 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/124 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/124 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/125 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/125 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/126 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/126 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/127 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/127 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/128 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/128 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/129 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/129 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/130 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/130 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/131 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/131 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/132 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/132 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/133 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/133 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/134 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/134 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/135 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/135 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/136 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/136 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/137 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/137 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/138 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/138 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/139 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/139 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/140 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/140 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/141 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/141 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/142 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/142 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/143 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/143 (1 ms) 9: [----------] 144 tests from SaneInput/PmeGatherTest (54 ms total) 9: 9: [----------] 16 tests from SaneInput/PmeSolveTest 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (2 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (3 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (2 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (21 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (3 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (2 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (2 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (2 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (0 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (1 ms) 9: [----------] 16 tests from SaneInput/PmeSolveTest (44 ms total) 9: 9: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (0 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (0 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (1 ms) 9: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (6 ms total) 9: 9: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (1 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (1 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (1 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (0 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (2 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (1 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (0 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (1 ms) 9: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (7 ms total) 9: 9: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (0 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (2 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (2 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (1 ms) 9: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (17 ms total) 9: 9: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (1 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (4 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (2 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (2 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (1 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (2 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (0 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (1 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (1 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (1 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (1 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (1 ms) 9: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (18 ms total) 9: 9: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (2 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (26 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (2 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (2 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (3 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (3 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (3 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (3 ms) 9: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (49 ms total) 9: 9: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (4 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (3 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (4 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (4 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (7 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (6 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (4 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (3 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (3 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (3 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (4 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (4 ms) 9: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (51 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 257 tests from 10 test cases ran. (522 ms total) 9: [ PASSED ] 257 tests. 9/54 Test #9: EwaldUnitTests ...................... Passed 0.59 sec test 10 Start 10: FFTUnitTests 10: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/fft-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/FFTUnitTests.xml" 10: Test timeout computed to be: 30 10: [==========] Running 14 tests from 4 test cases. 10: [----------] Global test environment set-up. 10: [----------] 2 tests from ManyFFTTest 10: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 10: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (6 ms) 10: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 10: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (27 ms) 10: [----------] 2 tests from ManyFFTTest (34 ms total) 10: 10: [----------] 1 test from FFTTest 10: [ RUN ] FFTTest.Real2DLength18_15Test 10: [ OK ] FFTTest.Real2DLength18_15Test (9 ms) 10: [----------] 1 test from FFTTest (10 ms total) 10: 10: [----------] 1 test from FFFTest3D 10: [ RUN ] FFFTest3D.Real5_6_9 10: [ OK ] FFFTest3D.Real5_6_9 (2 ms) 10: [----------] 1 test from FFFTest3D (3 ms total) 10: 10: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (1 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (1 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (2 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (6 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (4 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (1 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (1 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (1 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (22 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (20 ms) 10: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (79 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 14 tests from 4 test cases ran. (126 ms total) 10: [ PASSED ] 14 tests. 10/54 Test #10: FFTUnitTests ........................ Passed 0.14 sec test 11 Start 11: GpuUtilsUnitTests 11: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/gpu_utils-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/GpuUtilsUnitTests.xml" 11: Test timeout computed to be: 30 11: [==========] Running 62 tests from 20 test cases. 11: [----------] Global test environment set-up. 11: [----------] 2 tests from ClfftInitializer 11: [ RUN ] ClfftInitializer.SingleInitializationWorks 11: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) 11: [ RUN ] ClfftInitializer.TwoInitializationsWork 11: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) 11: [----------] 2 tests from ClfftInitializer (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 11: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 11: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 11: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 11: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float 11: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 11: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 11: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 11: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 11: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 11: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 11: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 11: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 11: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 11: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 11: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 11: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 11: 11: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 11: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 11: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 11: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 11: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 11: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 11: 11: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float 11: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 11: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 11: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 11: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 11: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 11: 11: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 11: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 11: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 11: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 11: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 11: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 11: 11: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 11: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 11: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 11: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 11: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/0.Swap 11: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/0.Comparison 11: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 11: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 11: 11: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float 11: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 11: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 11: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 11: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/1.Swap 11: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/1.Comparison 11: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 11: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 11: 11: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 11: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 11: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 11: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 11: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/2.Swap 11: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/2.Comparison 11: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 11: [----------] 5 tests from HostAllocatorTestNoMem/2 (1 ms total) 11: 11: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 11: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 11: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 11: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 11: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/3.Swap 11: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/3.Comparison 11: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 11: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 11: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 11: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 11: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float 11: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 11: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 11: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 11: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 11: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 11: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 11: 11: [----------] 1 test from HostAllocatorUntypedTest 11: [ RUN ] HostAllocatorUntypedTest.Comparison 11: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 11: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 11: 11: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 11: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/0.Move 11: [ OK ] AllocatorTest/0.Move (0 ms) 11: [----------] 4 tests from AllocatorTest/0 (0 ms total) 11: 11: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 11: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/1.Move 11: [ OK ] AllocatorTest/1.Move (0 ms) 11: [----------] 4 tests from AllocatorTest/1 (0 ms total) 11: 11: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 11: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/2.Move 11: [ OK ] AllocatorTest/2.Move (0 ms) 11: [----------] 4 tests from AllocatorTest/2 (0 ms total) 11: 11: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 11: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (1 ms) 11: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/3.Move 11: [ OK ] AllocatorTest/3.Move (0 ms) 11: [----------] 4 tests from AllocatorTest/3 (1 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 62 tests from 20 test cases ran. (2 ms total) 11: [ PASSED ] 62 tests. 11/54 Test #11: GpuUtilsUnitTests ................... Passed 0.02 sec test 12 Start 12: HardwareUnitTests 12: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/hardware-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/HardwareUnitTests.xml" 12: Test timeout computed to be: 30 12: [==========] Running 4 tests from 1 test case. 12: [----------] Global test environment set-up. 12: [----------] 4 tests from HardwareTopologyTest 12: [ RUN ] HardwareTopologyTest.Execute 12: [ OK ] HardwareTopologyTest.Execute (36 ms) 12: [ RUN ] HardwareTopologyTest.HwlocExecute 12: [ OK ] HardwareTopologyTest.HwlocExecute (76 ms) 12: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 12: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (40 ms) 12: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 12: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (36 ms) 12: [----------] 4 tests from HardwareTopologyTest (188 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 4 tests from 1 test case ran. (189 ms total) 12: [ PASSED ] 4 tests. 12/54 Test #12: HardwareUnitTests ................... Passed 0.23 sec test 13 Start 13: MathUnitTests 13: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/math-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/MathUnitTests.xml" 13: Test timeout computed to be: 30 13: [==========] Running 204 tests from 29 test cases. 13: [----------] Global test environment set-up. 13: [----------] 1 test from EmptyArrayRefWithPaddingTest 13: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 13: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 13: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 13: 13: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 13: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 13: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 13: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 13: 13: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 13: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 13: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 13: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 13: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 13: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 13: 13: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 13: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 13: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 13: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 13: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 13: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 13: 13: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 13: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 13: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 13: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 13: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 13: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 13: 13: [----------] 8 tests from TranslateAndScaleTest 13: [ RUN ] TranslateAndScaleTest.identityTransformation 13: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms) 13: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling 13: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) 13: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation 13: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) 13: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial 13: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms) 13: [ RUN ] TranslateAndScaleTest.scalingIdentity 13: [ OK ] TranslateAndScaleTest.scalingIdentity (1 ms) 13: [ RUN ] TranslateAndScaleTest.scalingNonTrivial 13: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) 13: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero 13: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms) 13: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero 13: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) 13: [----------] 8 tests from TranslateAndScaleTest (1 ms total) 13: 13: [----------] 12 tests from DensitySimilarityTest 13: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect 13: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect 13: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch 13: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms) 13: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch 13: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms) 13: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect 13: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero 13: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms) 13: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect 13: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect 13: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne 13: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (36 ms) 13: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated 13: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (54 ms) 13: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated 13: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (18 ms) 13: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect 13: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms) 13: [----------] 12 tests from DensitySimilarityTest (108 ms total) 13: 13: [----------] 6 tests from StructureSimilarityTest 13: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 13: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 13: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 13: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 13: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 13: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 13: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 13: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 13: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 13: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 13: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 13: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 13: [----------] 6 tests from StructureSimilarityTest (0 ms total) 13: 13: [----------] 8 tests from ExponentialMovingAverage 13: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero 13: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) 13: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative 13: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) 13: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue 13: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) 13: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue 13: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) 13: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly 13: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) 13: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing 13: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) 13: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect 13: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) 13: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree 13: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) 13: [----------] 8 tests from ExponentialMovingAverage (0 ms total) 13: 13: [----------] 21 tests from FunctionTest 13: [ RUN ] FunctionTest.StaticLog2 13: [ OK ] FunctionTest.StaticLog2 (0 ms) 13: [ RUN ] FunctionTest.Log2I32Bit 13: [ OK ] FunctionTest.Log2I32Bit (1 ms) 13: [ RUN ] FunctionTest.Log2I64Bit 13: [ OK ] FunctionTest.Log2I64Bit (0 ms) 13: [ RUN ] FunctionTest.GreatestCommonDivisor 13: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 13: [ RUN ] FunctionTest.InvsqrtFloat 13: [ OK ] FunctionTest.InvsqrtFloat (0 ms) 13: [ RUN ] FunctionTest.InvsqrtDouble 13: [ OK ] FunctionTest.InvsqrtDouble (1 ms) 13: [ RUN ] FunctionTest.InvsqrtInteger 13: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 13: [ RUN ] FunctionTest.InvcbrtFloat 13: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 13: [ RUN ] FunctionTest.InvcbrtDouble 13: [ OK ] FunctionTest.InvcbrtDouble (1 ms) 13: [ RUN ] FunctionTest.InvcbrtInteger 13: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 13: [ RUN ] FunctionTest.SixthrootFloat 13: [ OK ] FunctionTest.SixthrootFloat (0 ms) 13: [ RUN ] FunctionTest.SixthrootDouble 13: [ OK ] FunctionTest.SixthrootDouble (0 ms) 13: [ RUN ] FunctionTest.SixthrootInteger 13: [ OK ] FunctionTest.SixthrootInteger (0 ms) 13: [ RUN ] FunctionTest.InvsixthrootFloat 13: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 13: [ RUN ] FunctionTest.InvsixthrootDouble 13: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 13: [ RUN ] FunctionTest.InvsixthrootInteger 13: [ OK ] FunctionTest.InvsixthrootInteger (1 ms) 13: [ RUN ] FunctionTest.Powers 13: [ OK ] FunctionTest.Powers (0 ms) 13: [ RUN ] FunctionTest.ErfInvFloat 13: [ OK ] FunctionTest.ErfInvFloat (0 ms) 13: [ RUN ] FunctionTest.ErfInvDouble 13: [ OK ] FunctionTest.ErfInvDouble (0 ms) 13: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 13: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 13: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 13: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) 13: [----------] 21 tests from FunctionTest (4 ms total) 13: 13: [----------] 4 tests from GaussianOn1DLattice 13: [ RUN ] GaussianOn1DLattice.sumsCloseToOne 13: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) 13: [ RUN ] GaussianOn1DLattice.isCorrect 13: [ OK ] GaussianOn1DLattice.isCorrect (0 ms) 13: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero 13: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) 13: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange 13: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) 13: [----------] 4 tests from GaussianOn1DLattice (0 ms total) 13: 13: [----------] 9 tests from GaussTransformTest 13: [ RUN ] GaussTransformTest.isZeroUponConstruction 13: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) 13: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss 13: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) 13: [ RUN ] GaussTransformTest.isZeroAfterSettingZero 13: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) 13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX 13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) 13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY 13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) 13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ 13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) 13: [ RUN ] GaussTransformTest.complementaryGaussAddToZero 13: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) 13: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues 13: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms) 13: [ RUN ] GaussTransformTest.view 13: [ OK ] GaussTransformTest.view (0 ms) 13: [----------] 9 tests from GaussTransformTest (1 ms total) 13: 13: [----------] 3 tests from DensityFittingForce 13: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity 13: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) 13: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections 13: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) 13: [ RUN ] DensityFittingForce.pullsTowardsDerivative 13: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) 13: [----------] 3 tests from DensityFittingForce (0 ms total) 13: 13: [----------] 2 tests from InvertMatrixTest 13: [ RUN ] InvertMatrixTest.IdentityIsImpotent 13: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 13: [ RUN ] InvertMatrixTest.ComputesInverse 13: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 13: [----------] 2 tests from InvertMatrixTest (0 ms total) 13: 13: [----------] 2 tests from InvertBoxMatrixTest 13: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 13: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 13: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 13: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 13: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 13: 13: [----------] 15 tests from MatrixTest 13: [ RUN ] MatrixTest.canSetFromArray 13: [ OK ] MatrixTest.canSetFromArray (0 ms) 13: [ RUN ] MatrixTest.canSetStaticallyFromList 13: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) 13: [ RUN ] MatrixTest.canConstructAndFill 13: [ OK ] MatrixTest.canConstructAndFill (0 ms) 13: [ RUN ] MatrixTest.canSetValues 13: [ OK ] MatrixTest.canSetValues (0 ms) 13: [ RUN ] MatrixTest.canCopyAssign 13: [ OK ] MatrixTest.canCopyAssign (0 ms) 13: [ RUN ] MatrixTest.canSwap 13: [ OK ] MatrixTest.canSwap (0 ms) 13: [ RUN ] MatrixTest.staticMultiDimArrayExtent 13: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) 13: [ RUN ] MatrixTest.determinantWorks 13: [ OK ] MatrixTest.determinantWorks (0 ms) 13: [ RUN ] MatrixTest.noninvertableDeterminantIsZero 13: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) 13: [ RUN ] MatrixTest.determinantOfDiagonalMatrix 13: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) 13: [ RUN ] MatrixTest.traceWorks 13: [ OK ] MatrixTest.traceWorks (0 ms) 13: [ RUN ] MatrixTest.transposeWorks 13: [ OK ] MatrixTest.transposeWorks (0 ms) 13: [ RUN ] MatrixTest.transposeOfSymmetricMatrix 13: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) 13: [ RUN ] MatrixTest.canCreateFromLegacyMatrix 13: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) 13: [ RUN ] MatrixTest.canFillLegacyMatrix 13: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) 13: [----------] 15 tests from MatrixTest (0 ms total) 13: 13: [----------] 25 tests from MultiDimArrayTest 13: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic 13: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic 13: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canSetValuesInStatic 13: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic 13: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canMoveConstructStatic 13: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic 13: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canMoveAssignStatic 13: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic 13: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canCopyConstructStatic 13: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic 13: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canCopyAssignStatic 13: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic 13: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canSwapStatic 13: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canSwapDynamic 13: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent 13: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) 13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent 13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) 13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent 13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) 13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue 13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) 13: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray 13: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) 13: [ RUN ] MultiDimArrayTest.conversionToView 13: [ OK ] MultiDimArrayTest.conversionToView (0 ms) 13: [ RUN ] MultiDimArrayTest.conversionToConstView 13: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) 13: [ RUN ] MultiDimArrayTest.viewBegin 13: [ OK ] MultiDimArrayTest.viewBegin (0 ms) 13: [ RUN ] MultiDimArrayTest.viewEnd 13: [ OK ] MultiDimArrayTest.viewEnd (0 ms) 13: [ RUN ] MultiDimArrayTest.constViewConstBegin 13: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) 13: [ RUN ] MultiDimArrayTest.constViewConstEnd 13: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) 13: [----------] 25 tests from MultiDimArrayTest (0 ms total) 13: 13: [----------] 4 tests from MultiDimArrayToMdSpanTest 13: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan 13: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) 13: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan 13: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) 13: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan 13: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) 13: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan 13: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) 13: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/0, where TypeParam = std::allocator 13: [ RUN ] PaddedVectorTest/0.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/0.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/0.CanCopyAssign 13: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/0.CanMoveAssign 13: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/0.CanSwap 13: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/0 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/1, where TypeParam = std::allocator 13: [ RUN ] PaddedVectorTest/1.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/1.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/1.CanCopyAssign 13: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/1.CanMoveAssign 13: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/1.CanSwap 13: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/1 (1 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/2, where TypeParam = std::allocator 13: [ RUN ] PaddedVectorTest/2.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/2.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/2.CanCopyAssign 13: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/2.CanMoveAssign 13: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/2.CanSwap 13: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/2 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 13: [ RUN ] PaddedVectorTest/3.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/3.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/3.CanCopyAssign 13: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/3.CanMoveAssign 13: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/3.CanSwap 13: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/3 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 13: [ RUN ] PaddedVectorTest/4.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/4.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/4.CanCopyAssign 13: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/4.CanMoveAssign 13: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/4.CanSwap 13: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/4 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 13: [ RUN ] PaddedVectorTest/5.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/5.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/5.CanCopyAssign 13: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/5.CanMoveAssign 13: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/5.CanSwap 13: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/5 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 13: [ RUN ] PaddedVectorTest/6.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/6.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/6.CanCopyAssign 13: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/6.CanMoveAssign 13: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/6.CanSwap 13: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/6 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 13: [ RUN ] PaddedVectorTest/7.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/7.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/7.CanCopyAssign 13: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/7.CanMoveAssign 13: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/7.CanSwap 13: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/7 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 13: [ RUN ] PaddedVectorTest/8.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/8.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/8.CanCopyAssign 13: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/8.CanMoveAssign 13: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/8.CanSwap 13: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/8 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 13: [ RUN ] PaddedVectorTest/9.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/9.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/9.CanCopyAssign 13: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/9.CanMoveAssign 13: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/9.CanSwap 13: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/9 (0 ms total) 13: 13: [----------] 37 tests from RVecTest 13: [ RUN ] RVecTest.CanBeStoredInVector 13: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 13: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 13: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 13: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 13: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 13: [ RUN ] RVecTest.WorksAsMutable_rvec 13: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 13: [ RUN ] RVecTest.WorksAs_rvec_Array 13: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 13: [ RUN ] RVecTest.CanAddRVecToRvec 13: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 13: [ RUN ] RVecTest.CanAddAssignRVecToRvec 13: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 13: [ RUN ] RVecTest.CanSubtractRVecFromRvec 13: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 13: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 13: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 13: [ RUN ] RVecTest.CanDotProductRVecByRvec 13: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 13: [ RUN ] RVecTest.CanCrossProductRVecByRvec 13: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 13: [ RUN ] RVecTest.CanDivideRVecInplace 13: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 13: [ RUN ] RVecTest.CanScaleRVec 13: [ OK ] RVecTest.CanScaleRVec (0 ms) 13: [ RUN ] RVecTest.CanDivideRVec 13: [ OK ] RVecTest.CanDivideRVec (0 ms) 13: [ RUN ] RVecTest.CanDoUnitvFromRVec 13: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 13: [ RUN ] RVecTest.CanSqLengthOfRVec 13: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 13: [ RUN ] RVecTest.CanLengthOfRVec 13: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 13: [ RUN ] RVecTest.CanCastToRVec 13: [ OK ] RVecTest.CanCastToRVec (0 ms) 13: [ RUN ] RVecTest.CanCastToDVec 13: [ OK ] RVecTest.CanCastToDVec (0 ms) 13: [ RUN ] RVecTest.CanLeftScalarMultiply 13: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 13: [ RUN ] RVecTest.CanRightScalarMultiply 13: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 13: [ RUN ] RVecTest.CanGetUnitvFromRVec 13: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 13: [ RUN ] RVecTest.CanGetSqLengthOfRVec 13: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 13: [ RUN ] RVecTest.CanGetLengthOfRVec 13: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 13: [ RUN ] RVecTest.CanDoCrossProductOfRVec 13: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 13: [ RUN ] RVecTest.CanDoDotProductOfRVec 13: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 13: [ RUN ] RVecTest.CanScaleByVector 13: [ OK ] RVecTest.CanScaleByVector (0 ms) 13: [ RUN ] RVecTest.asIVec 13: [ OK ] RVecTest.asIVec (0 ms) 13: [ RUN ] RVecTest.elementWiseMin 13: [ OK ] RVecTest.elementWiseMin (0 ms) 13: [ RUN ] RVecTest.elementWiseMax 13: [ OK ] RVecTest.elementWiseMax (0 ms) 13: [ RUN ] RVecTest.WorksAs_dvec_Reference 13: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 13: [ RUN ] RVecTest.WorksAs_ivec_Reference 13: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 13: [ RUN ] RVecTest.WorksAs_rvec_Reference 13: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 13: [ RUN ] RVecTest.CopyConstructorWorks 13: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 13: [ RUN ] RVecTest.CopyAssignmentWorks 13: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 13: [ RUN ] RVecTest.MoveConstructorWorks 13: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 13: [ RUN ] RVecTest.MoveAssignmentWorks 13: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 13: [----------] 37 tests from RVecTest (0 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 204 tests from 29 test cases ran. (115 ms total) 13: [ PASSED ] 204 tests. 13/54 Test #13: MathUnitTests ....................... Passed 0.13 sec test 14 Start 14: MdrunUtilityUnitTests 14: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/mdrunutility-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/MdrunUtilityUnitTests.xml" 14: Test timeout computed to be: 30 14: [==========] Running 17 tests from 1 test case. 14: [----------] Global test environment set-up. 14: [----------] 17 tests from ThreadAffinityTest 14: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 14: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 14: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (1 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 14: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 14: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 14: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 14: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 14: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) 14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 14: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 14: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (1 ms) 14: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 14: NOTE: Affinity setting failed. 14: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) 14: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 14: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (0 ms) 14: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 14: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (0 ms) 14: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 14: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (0 ms) 14: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 14: NOTE: Affinity setting for 1/2 threads failed. 14: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (1 ms) 14: [----------] 17 tests from ThreadAffinityTest (3 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 17 tests from 1 test case ran. (3 ms total) 14: [ PASSED ] 17 tests. 14/54 Test #14: MdrunUtilityUnitTests ............... Passed 0.02 sec test 15 Start 15: MdrunUtilityMpiUnitTests 15: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 15: Test timeout computed to be: 30 15: [==========] Running 13 tests from 2 test cases. 15: [----------] Global test environment set-up. 15: [----------] 6 tests from ThreadAffinityMultiRankTest 15: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 15: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (6 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 15: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (5 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 15: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (1 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 15: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (1 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 15: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (1 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 15: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (1 ms) 15: [----------] 6 tests from ThreadAffinityMultiRankTest (15 ms total) 15: 15: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (1 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (1 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (1 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (0 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (1 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (1 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (1 ms) 15: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (6 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 13 tests from 2 test cases ran. (21 ms total) 15: [ PASSED ] 13 tests. 15/54 Test #15: MdrunUtilityMpiUnitTests ............ Passed 0.07 sec test 16 Start 16: MDSpanTests 16: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/mdspan-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/MDSpanTests.xml" 16: Test timeout computed to be: 30 16: [==========] Running 32 tests from 7 test cases. 16: [----------] Global test environment set-up. 16: [----------] 4 tests from BasicAccessorPolicy 16: [ RUN ] BasicAccessorPolicy.Decay 16: [ OK ] BasicAccessorPolicy.Decay (0 ms) 16: [ RUN ] BasicAccessorPolicy.Access 16: [ OK ] BasicAccessorPolicy.Access (0 ms) 16: [ RUN ] BasicAccessorPolicy.Offset 16: [ OK ] BasicAccessorPolicy.Offset (0 ms) 16: [ RUN ] BasicAccessorPolicy.CopyAccessor 16: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) 16: [----------] 4 tests from BasicAccessorPolicy (0 ms total) 16: 16: [----------] 4 tests from ExtentsTest 16: [ RUN ] ExtentsTest.Construction 16: [ OK ] ExtentsTest.Construction (0 ms) 16: [ RUN ] ExtentsTest.PurelyStatic 16: [ OK ] ExtentsTest.PurelyStatic (0 ms) 16: [ RUN ] ExtentsTest.RankNought 16: [ OK ] ExtentsTest.RankNought (0 ms) 16: [ RUN ] ExtentsTest.Assignment 16: [ OK ] ExtentsTest.Assignment (0 ms) 16: [----------] 4 tests from ExtentsTest (0 ms total) 16: 16: [----------] 8 tests from MdSpanExtension 16: [ RUN ] MdSpanExtension.SlicingAllStatic 16: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) 16: [ RUN ] MdSpanExtension.SlicingDynamic 16: [ OK ] MdSpanExtension.SlicingDynamic (0 ms) 16: [ RUN ] MdSpanExtension.SlicingAllStatic3D 16: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) 16: [ RUN ] MdSpanExtension.SlicingEqualsView3D 16: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) 16: [ RUN ] MdSpanExtension.additionWorks 16: [ OK ] MdSpanExtension.additionWorks (0 ms) 16: [ RUN ] MdSpanExtension.subtractionWorks 16: [ OK ] MdSpanExtension.subtractionWorks (0 ms) 16: [ RUN ] MdSpanExtension.multiplicationWorks 16: [ OK ] MdSpanExtension.multiplicationWorks (0 ms) 16: [ RUN ] MdSpanExtension.divisionWorks 16: [ OK ] MdSpanExtension.divisionWorks (0 ms) 16: [----------] 8 tests from MdSpanExtension (0 ms total) 16: 16: [----------] 3 tests from LayoutTests 16: [ RUN ] LayoutTests.LayoutRightConstruction 16: [ OK ] LayoutTests.LayoutRightConstruction (0 ms) 16: [ RUN ] LayoutTests.LayoutRightProperties 16: [ OK ] LayoutTests.LayoutRightProperties (0 ms) 16: [ RUN ] LayoutTests.LayoutRightOperator 16: [ OK ] LayoutTests.LayoutRightOperator (0 ms) 16: [----------] 3 tests from LayoutTests (0 ms total) 16: 16: [----------] 1 test from MdSpanTest 16: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly 16: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) 16: [----------] 1 test from MdSpanTest (0 ms total) 16: 16: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 16: [ RUN ] MdSpanTest/0.Rank 16: [ OK ] MdSpanTest/0.Rank (0 ms) 16: [ RUN ] MdSpanTest/0.DynamicRank 16: [ OK ] MdSpanTest/0.DynamicRank (0 ms) 16: [ RUN ] MdSpanTest/0.Extents 16: [ OK ] MdSpanTest/0.Extents (0 ms) 16: [ RUN ] MdSpanTest/0.Strides 16: [ OK ] MdSpanTest/0.Strides (0 ms) 16: [ RUN ] MdSpanTest/0.Properties 16: [ OK ] MdSpanTest/0.Properties (0 ms) 16: [ RUN ] MdSpanTest/0.Operator 16: [ OK ] MdSpanTest/0.Operator (0 ms) 16: [----------] 6 tests from MdSpanTest/0 (0 ms total) 16: 16: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 16: [ RUN ] MdSpanTest/1.Rank 16: [ OK ] MdSpanTest/1.Rank (0 ms) 16: [ RUN ] MdSpanTest/1.DynamicRank 16: [ OK ] MdSpanTest/1.DynamicRank (0 ms) 16: [ RUN ] MdSpanTest/1.Extents 16: [ OK ] MdSpanTest/1.Extents (0 ms) 16: [ RUN ] MdSpanTest/1.Strides 16: [ OK ] MdSpanTest/1.Strides (0 ms) 16: [ RUN ] MdSpanTest/1.Properties 16: [ OK ] MdSpanTest/1.Properties (0 ms) 16: [ RUN ] MdSpanTest/1.Operator 16: [ OK ] MdSpanTest/1.Operator (0 ms) 16: [----------] 6 tests from MdSpanTest/1 (1 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 32 tests from 7 test cases ran. (1 ms total) 16: [ PASSED ] 32 tests. 16/54 Test #16: MDSpanTests ......................... Passed 0.01 sec test 17 Start 17: OnlineHelpUnitTests 17: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/onlinehelp-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/OnlineHelpUnitTests.xml" 17: Test timeout computed to be: 30 17: [==========] Running 22 tests from 4 test cases. 17: [----------] Global test environment set-up. 17: [----------] 6 tests from TextTableFormatterTest 17: [ RUN ] TextTableFormatterTest.HandlesBasicCase 17: [ OK ] TextTableFormatterTest.HandlesBasicCase (1 ms) 17: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 17: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) 17: [ RUN ] TextTableFormatterTest.HandlesIndentation 17: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) 17: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 17: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) 17: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 17: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms) 17: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 17: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) 17: [----------] 6 tests from TextTableFormatterTest (1 ms total) 17: 17: [----------] 3 tests from HelpManagerTest 17: [ RUN ] HelpManagerTest.HandlesRootTopic 17: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 17: [ RUN ] HelpManagerTest.HandlesSubTopics 17: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 17: [ RUN ] HelpManagerTest.HandlesInvalidTopics 17: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 17: [----------] 3 tests from HelpManagerTest (0 ms total) 17: 17: [----------] 2 tests from HelpTopicFormattingTest 17: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 17: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms) 17: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 17: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) 17: [----------] 2 tests from HelpTopicFormattingTest (1 ms total) 17: 17: [----------] 11 tests from HelpWriterContextTest 17: [ RUN ] HelpWriterContextTest.FormatsParagraphs 17: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 17: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 17: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 17: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsLiteralText 17: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 17: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 17: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsBulletList 17: [ OK ] HelpWriterContextTest.FormatsBulletList (1 ms) 17: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 17: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 17: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsGridTable 17: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsTitles 17: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) 17: [----------] 11 tests from HelpWriterContextTest (1 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 22 tests from 4 test cases ran. (3 ms total) 17: [ PASSED ] 22 tests. 17/54 Test #17: OnlineHelpUnitTests ................. Passed 0.01 sec test 18 Start 18: OptionsUnitTests 18: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/options-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/OptionsUnitTests.xml" 18: Test timeout computed to be: 30 18: [==========] Running 110 tests from 18 test cases. 18: [----------] Global test environment set-up. 18: [----------] 5 tests from AbstractOptionStorageTest 18: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 18: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 18: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 18: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) 18: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 18: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 18: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 18: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 18: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 18: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 18: [----------] 5 tests from AbstractOptionStorageTest (0 ms total) 18: 18: [----------] 8 tests from FileNameOptionTest 18: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 18: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 18: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 18: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 18: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 18: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 18: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 18: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 18: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 18: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 18: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 18: [----------] 8 tests from FileNameOptionTest (0 ms total) 18: 18: [----------] 15 tests from FileNameOptionManagerTest 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 18: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 18: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 18: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 18: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 18: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 18: [----------] 15 tests from FileNameOptionManagerTest (1 ms total) 18: 18: [----------] 1 test from OptionsTest 18: [ RUN ] OptionsTest.FailsOnNonsafeStorage 18: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 18: [----------] 1 test from OptionsTest (0 ms total) 18: 18: [----------] 9 tests from OptionsAssignerTest 18: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 18: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 18: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 18: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 18: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesMissingValue 18: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesExtraValue 18: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesGroups 18: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesSections 18: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 18: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 18: [----------] 9 tests from OptionsAssignerTest (0 ms total) 18: 18: [----------] 4 tests from OptionsAssignerBooleanTest 18: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 18: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 18: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 18: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 18: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 18: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 18: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 18: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 18: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 18: 18: [----------] 13 tests from OptionsAssignerIntegerTest 18: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 18: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 18: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 18: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 18: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 18: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 18: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 18: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 18: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 18: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 18: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 18: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total) 18: 18: [----------] 5 tests from OptionsAssignerDoubleTest 18: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 18: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 18: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 18: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 18: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 18: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 18: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 18: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 18: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 18: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 18: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 18: 18: [----------] 9 tests from OptionsAssignerStringTest 18: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 18: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 18: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 18: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 18: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 18: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 18: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 18: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 18: 18: [----------] 6 tests from OptionsAssignerEnumTest 18: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 18: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 18: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 18: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 18: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 18: 18: [----------] 8 tests from RepeatingOptionSectionTest 18: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 18: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 18: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 18: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 18: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 18: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 18: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 18: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 18: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (1 ms) 18: [----------] 8 tests from RepeatingOptionSectionTest (1 ms total) 18: 18: [----------] 1 test from TimeUnitManagerTest 18: [ RUN ] TimeUnitManagerTest.BasicOperations 18: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 18: [----------] 1 test from TimeUnitManagerTest (0 ms total) 18: 18: [----------] 4 tests from TimeUnitBehaviorTest 18: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 18: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 18: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 18: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 18: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 18: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 18: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 18: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 18: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 18: 18: [----------] 2 tests from TreeValueSupportAssignTest 18: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 18: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 18: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 18: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 18: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) 18: 18: [----------] 1 test from TreeValueSupportAssignErrorTest 18: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 18: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 18: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 18: 18: [----------] 5 tests from TreeValueSupportCheckTest 18: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 18: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 18: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 18: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 18: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 18: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 18: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 18: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 18: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 18: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 18: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 18: 18: [----------] 6 tests from TreeValueSupportAdjustTest 18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (37 ms) 18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) 18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms) 18: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 18: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 18: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 18: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) 18: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 18: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 18: [----------] 6 tests from TreeValueSupportAdjustTest (37 ms total) 18: 18: [----------] 8 tests from TreeValueSupportTest 18: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 18: [ OK ] TreeValueSupportTest.SupportsBooleanOption (1 ms) 18: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 18: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsInt64Option 18: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsStringOption 18: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsFloatOption 18: [ OK ] TreeValueSupportTest.SupportsFloatOption (1 ms) 18: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 18: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsEnumIntOption 18: [ OK ] TreeValueSupportTest.SupportsEnumIntOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsEnumOption 18: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) 18: [----------] 8 tests from TreeValueSupportTest (2 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 110 tests from 18 test cases ran. (41 ms total) 18: [ PASSED ] 110 tests. 18/54 Test #18: OptionsUnitTests .................... Passed 0.06 sec test 19 Start 19: PbcutilUnitTest 19: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/pbcutil-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/PbcutilUnitTest.xml" 19: Test timeout computed to be: 30 19: [==========] Running 3 tests from 2 test cases. 19: [----------] Global test environment set-up. 19: [----------] 1 test from PbcTest 19: [ RUN ] PbcTest.CalcShiftsWorks 19: [ OK ] PbcTest.CalcShiftsWorks (1 ms) 19: [----------] 1 test from PbcTest (1 ms total) 19: 19: [----------] 2 tests from PbcEnumsTest 19: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect 19: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms) 19: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect 19: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) 19: [----------] 2 tests from PbcEnumsTest (0 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 3 tests from 2 test cases ran. (1 ms total) 19: [ PASSED ] 3 tests. 19/54 Test #19: PbcutilUnitTest ..................... Passed 0.01 sec test 20 Start 20: RandomUnitTests 20: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/random-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/RandomUnitTests.xml" 20: Test timeout computed to be: 30 20: [==========] Running 44 tests from 10 test cases. 20: [----------] Global test environment set-up. 20: [----------] 4 tests from ExponentialDistributionTest 20: [ RUN ] ExponentialDistributionTest.Output 20: [ OK ] ExponentialDistributionTest.Output (0 ms) 20: [ RUN ] ExponentialDistributionTest.Logical 20: [ OK ] ExponentialDistributionTest.Logical (0 ms) 20: [ RUN ] ExponentialDistributionTest.Reset 20: [ OK ] ExponentialDistributionTest.Reset (0 ms) 20: [ RUN ] ExponentialDistributionTest.AltParam 20: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 20: [----------] 4 tests from ExponentialDistributionTest (0 ms total) 20: 20: [----------] 4 tests from GammaDistributionTest 20: [ RUN ] GammaDistributionTest.Output 20: [ OK ] GammaDistributionTest.Output (0 ms) 20: [ RUN ] GammaDistributionTest.Logical 20: [ OK ] GammaDistributionTest.Logical (0 ms) 20: [ RUN ] GammaDistributionTest.Reset 20: [ OK ] GammaDistributionTest.Reset (0 ms) 20: [ RUN ] GammaDistributionTest.AltParam 20: [ OK ] GammaDistributionTest.AltParam (0 ms) 20: [----------] 4 tests from GammaDistributionTest (0 ms total) 20: 20: [----------] 4 tests from NormalDistributionTest 20: [ RUN ] NormalDistributionTest.Output 20: [ OK ] NormalDistributionTest.Output (0 ms) 20: [ RUN ] NormalDistributionTest.Logical 20: [ OK ] NormalDistributionTest.Logical (0 ms) 20: [ RUN ] NormalDistributionTest.Reset 20: [ OK ] NormalDistributionTest.Reset (0 ms) 20: [ RUN ] NormalDistributionTest.AltParam 20: [ OK ] NormalDistributionTest.AltParam (0 ms) 20: [----------] 4 tests from NormalDistributionTest (0 ms total) 20: 20: [----------] 1 test from SeedTest 20: [ RUN ] SeedTest.makeRandomSeed 20: [ OK ] SeedTest.makeRandomSeed (0 ms) 20: [----------] 1 test from SeedTest (0 ms total) 20: 20: [----------] 6 tests from TabulatedNormalDistributionTest 20: [ RUN ] TabulatedNormalDistributionTest.Output14 20: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) 20: [ RUN ] TabulatedNormalDistributionTest.Output16 20: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) 20: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 20: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (1 ms) 20: [ RUN ] TabulatedNormalDistributionTest.Logical 20: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 20: [ RUN ] TabulatedNormalDistributionTest.Reset 20: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 20: [ RUN ] TabulatedNormalDistributionTest.AltParam 20: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 20: [----------] 6 tests from TabulatedNormalDistributionTest (1 ms total) 20: 20: [----------] 1 test from TabulatedNormalDistributionTableTest 20: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 20: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (1 ms) 20: [----------] 1 test from TabulatedNormalDistributionTableTest (1 ms total) 20: 20: [----------] 6 tests from ThreeFry2x64Test 20: [ RUN ] ThreeFry2x64Test.Logical 20: [ OK ] ThreeFry2x64Test.Logical (0 ms) 20: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 20: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) 20: [ RUN ] ThreeFry2x64Test.Reseed 20: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 20: [ RUN ] ThreeFry2x64Test.Discard 20: [ OK ] ThreeFry2x64Test.Discard (0 ms) 20: [ RUN ] ThreeFry2x64Test.InvalidCounter 20: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 20: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 20: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 20: [----------] 6 tests from ThreeFry2x64Test (0 ms total) 20: 20: [----------] 4 tests from UniformIntDistributionTest 20: [ RUN ] UniformIntDistributionTest.Output 20: [ OK ] UniformIntDistributionTest.Output (0 ms) 20: [ RUN ] UniformIntDistributionTest.Logical 20: [ OK ] UniformIntDistributionTest.Logical (0 ms) 20: [ RUN ] UniformIntDistributionTest.Reset 20: [ OK ] UniformIntDistributionTest.Reset (0 ms) 20: [ RUN ] UniformIntDistributionTest.AltParam 20: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 20: [----------] 4 tests from UniformIntDistributionTest (0 ms total) 20: 20: [----------] 5 tests from UniformRealDistributionTest 20: [ RUN ] UniformRealDistributionTest.GenerateCanonical 20: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 20: [ RUN ] UniformRealDistributionTest.Output 20: [ OK ] UniformRealDistributionTest.Output (0 ms) 20: [ RUN ] UniformRealDistributionTest.Logical 20: [ OK ] UniformRealDistributionTest.Logical (0 ms) 20: [ RUN ] UniformRealDistributionTest.Reset 20: [ OK ] UniformRealDistributionTest.Reset (0 ms) 20: [ RUN ] UniformRealDistributionTest.AltParam 20: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 20: [----------] 5 tests from UniformRealDistributionTest (0 ms total) 20: 20: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (1 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 20: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (1 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 44 tests from 10 test cases ran. (3 ms total) 20: [ PASSED ] 44 tests. 20/54 Test #20: RandomUnitTests ..................... Passed 0.02 sec test 21 Start 21: RestraintTests 21: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/restraintpotential-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/RestraintTests.xml" 21: Test timeout computed to be: 30 21: [==========] Running 1 test from 1 test case. 21: [----------] Global test environment set-up. 21: [----------] 1 test from RestraintManager 21: [ RUN ] RestraintManager.restraintList 21: [ OK ] RestraintManager.restraintList (0 ms) 21: [----------] 1 test from RestraintManager (0 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 1 test from 1 test case ran. (0 ms total) 21: [ PASSED ] 1 test. 21/54 Test #21: RestraintTests ...................... Passed 0.01 sec test 22 Start 22: TableUnitTests 22: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/table-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/TableUnitTests.xml" 22: Test timeout computed to be: 30 22: [==========] Running 20 tests from 2 test cases. 22: [----------] Global test environment set-up. 22: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 22: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 22: [ OK ] SplineTableTest/0.HandlesIncorrectInput (2 ms) 22: [ RUN ] SplineTableTest/0.Sinc 22: [ OK ] SplineTableTest/0.Sinc (0 ms) 22: [ RUN ] SplineTableTest/0.LJ12 22: [ OK ] SplineTableTest/0.LJ12 (12 ms) 22: [ RUN ] SplineTableTest/0.PmeCorrection 22: [ OK ] SplineTableTest/0.PmeCorrection (26 ms) 22: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 22: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (1 ms) 22: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 22: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (1 ms) 22: [ RUN ] SplineTableTest/0.TwoFunctions 22: [ OK ] SplineTableTest/0.TwoFunctions (29 ms) 22: [ RUN ] SplineTableTest/0.ThreeFunctions 22: [ OK ] SplineTableTest/0.ThreeFunctions (31 ms) 22: [ RUN ] SplineTableTest/0.Simd 22: [ OK ] SplineTableTest/0.Simd (7 ms) 22: [ RUN ] SplineTableTest/0.SimdTwoFunctions 22: [ OK ] SplineTableTest/0.SimdTwoFunctions (49 ms) 22: [----------] 10 tests from SplineTableTest/0 (159 ms total) 22: 22: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 22: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 22: [ OK ] SplineTableTest/1.HandlesIncorrectInput (2 ms) 22: [ RUN ] SplineTableTest/1.Sinc 22: [ OK ] SplineTableTest/1.Sinc (0 ms) 22: [ RUN ] SplineTableTest/1.LJ12 22: [ OK ] SplineTableTest/1.LJ12 (3 ms) 22: [ RUN ] SplineTableTest/1.PmeCorrection 22: [ OK ] SplineTableTest/1.PmeCorrection (1 ms) 22: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 22: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms) 22: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 22: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (1 ms) 22: [ RUN ] SplineTableTest/1.TwoFunctions 22: [ OK ] SplineTableTest/1.TwoFunctions (5 ms) 22: [ RUN ] SplineTableTest/1.ThreeFunctions 22: [ OK ] SplineTableTest/1.ThreeFunctions (5 ms) 22: [ RUN ] SplineTableTest/1.Simd 22: [ OK ] SplineTableTest/1.Simd (1 ms) 22: [ RUN ] SplineTableTest/1.SimdTwoFunctions 22: [ OK ] SplineTableTest/1.SimdTwoFunctions (4 ms) 22: [----------] 10 tests from SplineTableTest/1 (22 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 20 tests from 2 test cases ran. (181 ms total) 22: [ PASSED ] 20 tests. 22/54 Test #22: TableUnitTests ...................... Passed 0.19 sec test 23 Start 23: TaskAssignmentUnitTests 23: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/taskassignment-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/TaskAssignmentUnitTests.xml" 23: Test timeout computed to be: 30 23: [==========] Running 3 tests from 2 test cases. 23: [----------] Global test environment set-up. 23: [----------] 2 tests from UserTaskAssignmentStringHandlingTest 23: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork 23: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms) 23: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid 23: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) 23: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total) 23: 23: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest 23: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow 23: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (0 ms) 23: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (0 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 3 tests from 2 test cases ran. (0 ms total) 23: [ PASSED ] 3 tests. 23/54 Test #23: TaskAssignmentUnitTests ............. Passed 0.01 sec test 24 Start 24: TopologyTest 24: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/topology-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/TopologyTest.xml" 24: Test timeout computed to be: 30 24: [==========] Running 11 tests from 3 test cases. 24: [----------] Global test environment set-up. 24: [----------] 3 tests from ExclusionBlockTest 24: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks 24: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) 24: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka 24: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) 24: [ RUN ] ExclusionBlockTest.MergeExclusions 24: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) 24: [----------] 3 tests from ExclusionBlockTest (0 ms total) 24: 24: [----------] 2 tests from MtopTest 24: [ RUN ] MtopTest.RangeBasedLoop 24: [ OK ] MtopTest.RangeBasedLoop (0 ms) 24: [ RUN ] MtopTest.Operators 24: [ OK ] MtopTest.Operators (0 ms) 24: [----------] 2 tests from MtopTest (0 ms total) 24: 24: [----------] 6 tests from SymtabTest 24: [ RUN ] SymtabTest.EmptyOnOpen 24: [ OK ] SymtabTest.EmptyOnOpen (0 ms) 24: [ RUN ] SymtabTest.AddSingleEntry 24: [ OK ] SymtabTest.AddSingleEntry (0 ms) 24: [ RUN ] SymtabTest.AddTwoDistinctEntries 24: [ OK ] SymtabTest.AddTwoDistinctEntries (0 ms) 24: [ RUN ] SymtabTest.TryToAddDuplicates 24: [ OK ] SymtabTest.TryToAddDuplicates (0 ms) 24: [ RUN ] SymtabTest.AddLargeNumberOfEntries 24: [ OK ] SymtabTest.AddLargeNumberOfEntries (0 ms) 24: [ RUN ] SymtabTest.NoDuplicatesInLargeTable 24: [ OK ] SymtabTest.NoDuplicatesInLargeTable (1 ms) 24: [----------] 6 tests from SymtabTest (1 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 11 tests from 3 test cases ran. (1 ms total) 24: [ PASSED ] 11 tests. 24/54 Test #24: TopologyTest ........................ Passed 0.01 sec test 25 Start 25: PullTest 25: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/pull-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/PullTest.xml" 25: Test timeout computed to be: 30 25: [==========] Running 5 tests from 1 test case. 25: [----------] Global test environment set-up. 25: [----------] 5 tests from PullTest 25: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 25: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 25: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 25: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 25: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 25: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 25: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 25: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 25: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 25: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 25: [----------] 5 tests from PullTest (0 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 5 tests from 1 test case ran. (0 ms total) 25: [ PASSED ] 5 tests. 25/54 Test #25: PullTest ............................ Passed 0.04 sec test 26 Start 26: AwhTest 26: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/awh-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/AwhTest.xml" 26: Test timeout computed to be: 30 26: [==========] Running 12 tests from 4 test cases. 26: [----------] Global test environment set-up. 26: [----------] 1 test from BiasTest 26: [ RUN ] BiasTest.DetectsCovering 26: [ OK ] BiasTest.DetectsCovering (1 ms) 26: [----------] 1 test from BiasTest (1 ms total) 26: 26: [----------] 1 test from gridTest 26: [ RUN ] gridTest.neighborhood 26: [ OK ] gridTest.neighborhood (2 ms) 26: [----------] 1 test from gridTest (2 ms total) 26: 26: [----------] 8 tests from WithParameters/BiasTest 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (1 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (1 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (0 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (1 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (1 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (1 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (1 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (0 ms) 26: [----------] 8 tests from WithParameters/BiasTest (7 ms total) 26: 26: [----------] 2 tests from WithParameters/BiasStateTest 26: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 26: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms) 26: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 26: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms) 26: [----------] 2 tests from WithParameters/BiasStateTest (0 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 12 tests from 4 test cases ran. (10 ms total) 26: [ PASSED ] 12 tests. 26/54 Test #26: AwhTest ............................. Passed 0.03 sec test 27 Start 27: SimdUnitTests 27: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/simd-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/SimdUnitTests.xml" 27: Test timeout computed to be: 30 27: [==========] Running 288 tests from 22 test cases. 27: [----------] Global test environment set-up. 27: [----------] 9 tests from SimdBootstrapTest 27: [ RUN ] SimdBootstrapTest.loadStore 27: [ OK ] SimdBootstrapTest.loadStore (0 ms) 27: [ RUN ] SimdBootstrapTest.loadU 27: [ OK ] SimdBootstrapTest.loadU (0 ms) 27: [ RUN ] SimdBootstrapTest.storeU 27: [ OK ] SimdBootstrapTest.storeU (0 ms) 27: [ RUN ] SimdBootstrapTest.loadStoreI 27: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) 27: [ RUN ] SimdBootstrapTest.loadUI 27: [ OK ] SimdBootstrapTest.loadUI (0 ms) 27: [ RUN ] SimdBootstrapTest.storeUI 27: [ OK ] SimdBootstrapTest.storeUI (0 ms) 27: [ RUN ] SimdBootstrapTest.simd4LoadStore 27: [ OK ] SimdBootstrapTest.simd4LoadStore (0 ms) 27: [ RUN ] SimdBootstrapTest.simd4LoadU 27: [ OK ] SimdBootstrapTest.simd4LoadU (0 ms) 27: [ RUN ] SimdBootstrapTest.simd4StoreU 27: [ OK ] SimdBootstrapTest.simd4StoreU (0 ms) 27: [----------] 9 tests from SimdBootstrapTest (0 ms total) 27: 27: [----------] 1 test from SimdTest 27: [ RUN ] SimdTest.GmxAligned 27: [ OK ] SimdTest.GmxAligned (0 ms) 27: [----------] 1 test from SimdTest (0 ms total) 27: 27: [----------] 42 tests from SimdFloatingpointTest 27: [ RUN ] SimdFloatingpointTest.setZero 27: [ OK ] SimdFloatingpointTest.setZero (0 ms) 27: [ RUN ] SimdFloatingpointTest.set 27: [ OK ] SimdFloatingpointTest.set (0 ms) 27: [ RUN ] SimdFloatingpointTest.add 27: [ OK ] SimdFloatingpointTest.add (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskAdd 27: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) 27: [ RUN ] SimdFloatingpointTest.sub 27: [ OK ] SimdFloatingpointTest.sub (0 ms) 27: [ RUN ] SimdFloatingpointTest.mul 27: [ OK ] SimdFloatingpointTest.mul (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskzMul 27: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) 27: [ RUN ] SimdFloatingpointTest.fma 27: [ OK ] SimdFloatingpointTest.fma (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskzFma 27: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) 27: [ RUN ] SimdFloatingpointTest.fms 27: [ OK ] SimdFloatingpointTest.fms (0 ms) 27: [ RUN ] SimdFloatingpointTest.fnma 27: [ OK ] SimdFloatingpointTest.fnma (0 ms) 27: [ RUN ] SimdFloatingpointTest.fnms 27: [ OK ] SimdFloatingpointTest.fnms (0 ms) 27: [ RUN ] SimdFloatingpointTest.abs 27: [ OK ] SimdFloatingpointTest.abs (0 ms) 27: [ RUN ] SimdFloatingpointTest.neg 27: [ OK ] SimdFloatingpointTest.neg (0 ms) 27: [ RUN ] SimdFloatingpointTest.and 27: [ OK ] SimdFloatingpointTest.and (0 ms) 27: [ RUN ] SimdFloatingpointTest.or 27: [ OK ] SimdFloatingpointTest.or (0 ms) 27: [ RUN ] SimdFloatingpointTest.xor 27: [ OK ] SimdFloatingpointTest.xor (0 ms) 27: [ RUN ] SimdFloatingpointTest.andNot 27: [ OK ] SimdFloatingpointTest.andNot (0 ms) 27: [ RUN ] SimdFloatingpointTest.max 27: [ OK ] SimdFloatingpointTest.max (0 ms) 27: [ RUN ] SimdFloatingpointTest.min 27: [ OK ] SimdFloatingpointTest.min (0 ms) 27: [ RUN ] SimdFloatingpointTest.round 27: [ OK ] SimdFloatingpointTest.round (0 ms) 27: [ RUN ] SimdFloatingpointTest.roundMode 27: [ OK ] SimdFloatingpointTest.roundMode (0 ms) 27: [ RUN ] SimdFloatingpointTest.trunc 27: [ OK ] SimdFloatingpointTest.trunc (0 ms) 27: [ RUN ] SimdFloatingpointTest.frexp 27: [ OK ] SimdFloatingpointTest.frexp (0 ms) 27: [ RUN ] SimdFloatingpointTest.ldexp 27: [ OK ] SimdFloatingpointTest.ldexp (0 ms) 27: [ RUN ] SimdFloatingpointTest.rsqrt 27: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskzRsqrt 27: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) 27: [ RUN ] SimdFloatingpointTest.rcp 27: [ OK ] SimdFloatingpointTest.rcp (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskzRcp 27: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) 27: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask 27: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) 27: [ RUN ] SimdFloatingpointTest.selectByNotMask 27: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) 27: [ RUN ] SimdFloatingpointTest.cmpNe 27: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) 27: [ RUN ] SimdFloatingpointTest.cmpLe 27: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) 27: [ RUN ] SimdFloatingpointTest.cmpLt 27: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) 27: [ RUN ] SimdFloatingpointTest.testBits 27: [ OK ] SimdFloatingpointTest.testBits (0 ms) 27: [ RUN ] SimdFloatingpointTest.andB 27: [ OK ] SimdFloatingpointTest.andB (0 ms) 27: [ RUN ] SimdFloatingpointTest.orB 27: [ OK ] SimdFloatingpointTest.orB (0 ms) 27: [ RUN ] SimdFloatingpointTest.anyTrueB 27: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) 27: [ RUN ] SimdFloatingpointTest.blend 27: [ OK ] SimdFloatingpointTest.blend (0 ms) 27: [ RUN ] SimdFloatingpointTest.reduce 27: [ OK ] SimdFloatingpointTest.reduce (0 ms) 27: [ RUN ] SimdFloatingpointTest.cvtFloat2Double 27: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) 27: [ RUN ] SimdFloatingpointTest.cvtDouble2Float 27: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) 27: [----------] 42 tests from SimdFloatingpointTest (0 ms total) 27: 27: [----------] 16 tests from SimdFloatingpointUtilTest 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets 27: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum 27: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.loadUNDuplicate4 27: [ OK ] SimdFloatingpointUtilTest.loadUNDuplicate4 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.load4DuplicateN 27: [ OK ] SimdFloatingpointUtilTest.load4DuplicateN (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.loadU4NOffset 27: [ OK ] SimdFloatingpointUtilTest.loadU4NOffset (0 ms) 27: [----------] 16 tests from SimdFloatingpointUtilTest (0 ms total) 27: 27: [----------] 3 tests from SimdVectorOperationsTest 27: [ RUN ] SimdVectorOperationsTest.iprod 27: [ OK ] SimdVectorOperationsTest.iprod (0 ms) 27: [ RUN ] SimdVectorOperationsTest.norm2 27: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) 27: [ RUN ] SimdVectorOperationsTest.cprod 27: [ OK ] SimdVectorOperationsTest.cprod (0 ms) 27: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) 27: 27: [----------] 56 tests from SimdMathTest 27: [ RUN ] SimdMathTest.generateTestPointsFloat 27: [ OK ] SimdMathTest.generateTestPointsFloat (0 ms) 27: [ RUN ] SimdMathTest.copysign 27: [ OK ] SimdMathTest.copysign (0 ms) 27: [ RUN ] SimdMathTest.invsqrt 27: [ OK ] SimdMathTest.invsqrt (0 ms) 27: [ RUN ] SimdMathTest.maskzInvsqrt 27: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) 27: [ RUN ] SimdMathTest.invsqrtPair 27: [ OK ] SimdMathTest.invsqrtPair (1 ms) 27: [ RUN ] SimdMathTest.sqrt 27: [ OK ] SimdMathTest.sqrt (0 ms) 27: [ RUN ] SimdMathTest.sqrtUnsafe 27: [ OK ] SimdMathTest.sqrtUnsafe (0 ms) 27: [ RUN ] SimdMathTest.inv 27: [ OK ] SimdMathTest.inv (3 ms) 27: [ RUN ] SimdMathTest.maskzInv 27: [ OK ] SimdMathTest.maskzInv (0 ms) 27: [ RUN ] SimdMathTest.cbrt 27: [ OK ] SimdMathTest.cbrt (0 ms) 27: [ RUN ] SimdMathTest.invcbrt 27: [ OK ] SimdMathTest.invcbrt (2 ms) 27: [ RUN ] SimdMathTest.log2 27: [ OK ] SimdMathTest.log2 (0 ms) 27: [ RUN ] SimdMathTest.log 27: [ OK ] SimdMathTest.log (0 ms) 27: [ RUN ] SimdMathTest.exp2 27: [ OK ] SimdMathTest.exp2 (2 ms) 27: [ RUN ] SimdMathTest.exp2Unsafe 27: [ OK ] SimdMathTest.exp2Unsafe (0 ms) 27: [ RUN ] SimdMathTest.exp 27: [ OK ] SimdMathTest.exp (1 ms) 27: [ RUN ] SimdMathTest.expUnsafe 27: [ OK ] SimdMathTest.expUnsafe (1 ms) 27: [ RUN ] SimdMathTest.pow 27: [ OK ] SimdMathTest.pow (0 ms) 27: [ RUN ] SimdMathTest.powUnsafe 27: [ OK ] SimdMathTest.powUnsafe (0 ms) 27: [ RUN ] SimdMathTest.erf 27: [ OK ] SimdMathTest.erf (0 ms) 27: [ RUN ] SimdMathTest.erfc 27: [ OK ] SimdMathTest.erfc (1 ms) 27: [ RUN ] SimdMathTest.sin 27: [ OK ] SimdMathTest.sin (1 ms) 27: [ RUN ] SimdMathTest.cos 27: [ OK ] SimdMathTest.cos (1 ms) 27: [ RUN ] SimdMathTest.tan 27: [ OK ] SimdMathTest.tan (1 ms) 27: [ RUN ] SimdMathTest.asin 27: [ OK ] SimdMathTest.asin (1 ms) 27: [ RUN ] SimdMathTest.acos 27: [ OK ] SimdMathTest.acos (0 ms) 27: [ RUN ] SimdMathTest.atan 27: [ OK ] SimdMathTest.atan (1 ms) 27: [ RUN ] SimdMathTest.atan2 27: [ OK ] SimdMathTest.atan2 (0 ms) 27: [ RUN ] SimdMathTest.pmeForceCorrection 27: [ OK ] SimdMathTest.pmeForceCorrection (0 ms) 27: [ RUN ] SimdMathTest.pmePotentialCorrection 27: [ OK ] SimdMathTest.pmePotentialCorrection (1 ms) 27: [ RUN ] SimdMathTest.invsqrtSingleAccuracy 27: [ OK ] SimdMathTest.invsqrtSingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy 27: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.sqrtSingleAccuracy 27: [ OK ] SimdMathTest.sqrtSingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe 27: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (1 ms) 27: [ RUN ] SimdMathTest.invSingleAccuracy 27: [ OK ] SimdMathTest.invSingleAccuracy (2 ms) 27: [ RUN ] SimdMathTest.cbrtSingleAccuracy 27: [ OK ] SimdMathTest.cbrtSingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.invcbrtSingleAccuracy 27: [ OK ] SimdMathTest.invcbrtSingleAccuracy (2 ms) 27: [ RUN ] SimdMathTest.log2SingleAccuracy 27: [ OK ] SimdMathTest.log2SingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.logSingleAccuracy 27: [ OK ] SimdMathTest.logSingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.exp2SingleAccuracy 27: [ OK ] SimdMathTest.exp2SingleAccuracy (2 ms) 27: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 27: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (0 ms) 27: [ RUN ] SimdMathTest.expSingleAccuracy 27: [ OK ] SimdMathTest.expSingleAccuracy (26 ms) 27: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe 27: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (1 ms) 27: [ RUN ] SimdMathTest.powSingleAccuracy 27: [ OK ] SimdMathTest.powSingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.powSingleAccuracyUnsafe 27: [ OK ] SimdMathTest.powSingleAccuracyUnsafe (0 ms) 27: [ RUN ] SimdMathTest.erfSingleAccuracy 27: [ OK ] SimdMathTest.erfSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.erfcSingleAccuracy 27: [ OK ] SimdMathTest.erfcSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.sinSingleAccuracy 27: [ OK ] SimdMathTest.sinSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.cosSingleAccuracy 27: [ OK ] SimdMathTest.cosSingleAccuracy (2 ms) 27: [ RUN ] SimdMathTest.tanSingleAccuracy 27: [ OK ] SimdMathTest.tanSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.asinSingleAccuracy 27: [ OK ] SimdMathTest.asinSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.acosSingleAccuracy 27: [ OK ] SimdMathTest.acosSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.atanSingleAccuracy 27: [ OK ] SimdMathTest.atanSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.atan2SingleAccuracy 27: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy 27: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 27: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (1 ms) 27: [----------] 56 tests from SimdMathTest (64 ms total) 27: 27: [----------] 1 test from EmptyArrayRefTest 27: [ RUN ] EmptyArrayRefTest.IsEmpty 27: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 27: [----------] 1 test from EmptyArrayRefTest (0 ms total) 27: 27: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 27: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 27: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks 27: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) 27: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks 27: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) 27: [----------] 3 tests from ArrayRefTest/0 (0 ms total) 27: 27: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 27: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 27: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks 27: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) 27: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks 27: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) 27: [----------] 3 tests from ArrayRefTest/1 (0 ms total) 27: 27: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 27: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 27: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks 27: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) 27: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks 27: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) 27: [----------] 3 tests from ArrayRefTest/2 (0 ms total) 27: 27: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 27: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 27: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks 27: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) 27: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks 27: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) 27: [----------] 3 tests from ArrayRefTest/3 (0 ms total) 27: 27: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefReadWriteTest/0.Assignment 27: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) 27: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) 27: 27: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefReadWriteTest/1.Assignment 27: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) 27: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) 27: 27: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefArithmeticTest/0.Basic 27: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) 27: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) 27: 27: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefArithmeticTest/1.Basic 27: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) 27: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) 27: 27: [----------] 23 tests from SimdIntegerTest 27: [ RUN ] SimdIntegerTest.setZero 27: [ OK ] SimdIntegerTest.setZero (0 ms) 27: [ RUN ] SimdIntegerTest.set 27: [ OK ] SimdIntegerTest.set (0 ms) 27: [ RUN ] SimdIntegerTest.add 27: [ OK ] SimdIntegerTest.add (0 ms) 27: [ RUN ] SimdIntegerTest.sub 27: [ OK ] SimdIntegerTest.sub (0 ms) 27: [ RUN ] SimdIntegerTest.mul 27: [ OK ] SimdIntegerTest.mul (0 ms) 27: [ RUN ] SimdIntegerTest.and 27: [ OK ] SimdIntegerTest.and (0 ms) 27: [ RUN ] SimdIntegerTest.andNot 27: [ OK ] SimdIntegerTest.andNot (0 ms) 27: [ RUN ] SimdIntegerTest.or 27: [ OK ] SimdIntegerTest.or (0 ms) 27: [ RUN ] SimdIntegerTest.xor 27: [ OK ] SimdIntegerTest.xor (0 ms) 27: [ RUN ] SimdIntegerTest.extract 27: [ OK ] SimdIntegerTest.extract (0 ms) 27: [ RUN ] SimdIntegerTest.cvtR2I 27: [ OK ] SimdIntegerTest.cvtR2I (0 ms) 27: [ RUN ] SimdIntegerTest.cvttR2I 27: [ OK ] SimdIntegerTest.cvttR2I (0 ms) 27: [ RUN ] SimdIntegerTest.cvtI2R 27: [ OK ] SimdIntegerTest.cvtI2R (0 ms) 27: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask 27: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) 27: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask 27: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) 27: [ RUN ] SimdIntegerTest.cmpLt 27: [ OK ] SimdIntegerTest.cmpLt (0 ms) 27: [ RUN ] SimdIntegerTest.testBits 27: [ OK ] SimdIntegerTest.testBits (0 ms) 27: [ RUN ] SimdIntegerTest.andB 27: [ OK ] SimdIntegerTest.andB (0 ms) 27: [ RUN ] SimdIntegerTest.orB 27: [ OK ] SimdIntegerTest.orB (0 ms) 27: [ RUN ] SimdIntegerTest.anyTrue 27: [ OK ] SimdIntegerTest.anyTrue (0 ms) 27: [ RUN ] SimdIntegerTest.blend 27: [ OK ] SimdIntegerTest.blend (0 ms) 27: [ RUN ] SimdIntegerTest.cvtB2IB 27: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) 27: [ RUN ] SimdIntegerTest.cvtIB2B 27: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) 27: [----------] 23 tests from SimdIntegerTest (0 ms total) 27: 27: [----------] 32 tests from Simd4FloatingpointTest 27: [ RUN ] Simd4FloatingpointTest.setZero 27: [ OK ] Simd4FloatingpointTest.setZero (0 ms) 27: [ RUN ] Simd4FloatingpointTest.set 27: [ OK ] Simd4FloatingpointTest.set (0 ms) 27: [ RUN ] Simd4FloatingpointTest.add 27: [ OK ] Simd4FloatingpointTest.add (0 ms) 27: [ RUN ] Simd4FloatingpointTest.sub 27: [ OK ] Simd4FloatingpointTest.sub (0 ms) 27: [ RUN ] Simd4FloatingpointTest.mul 27: [ OK ] Simd4FloatingpointTest.mul (0 ms) 27: [ RUN ] Simd4FloatingpointTest.fma 27: [ OK ] Simd4FloatingpointTest.fma (0 ms) 27: [ RUN ] Simd4FloatingpointTest.fms 27: [ OK ] Simd4FloatingpointTest.fms (0 ms) 27: [ RUN ] Simd4FloatingpointTest.fnma 27: [ OK ] Simd4FloatingpointTest.fnma (0 ms) 27: [ RUN ] Simd4FloatingpointTest.fnms 27: [ OK ] Simd4FloatingpointTest.fnms (0 ms) 27: [ RUN ] Simd4FloatingpointTest.abs 27: [ OK ] Simd4FloatingpointTest.abs (0 ms) 27: [ RUN ] Simd4FloatingpointTest.neg 27: [ OK ] Simd4FloatingpointTest.neg (0 ms) 27: [ RUN ] Simd4FloatingpointTest.and 27: [ OK ] Simd4FloatingpointTest.and (0 ms) 27: [ RUN ] Simd4FloatingpointTest.or 27: [ OK ] Simd4FloatingpointTest.or (0 ms) 27: [ RUN ] Simd4FloatingpointTest.xor 27: [ OK ] Simd4FloatingpointTest.xor (0 ms) 27: [ RUN ] Simd4FloatingpointTest.andNot 27: [ OK ] Simd4FloatingpointTest.andNot (0 ms) 27: [ RUN ] Simd4FloatingpointTest.max 27: [ OK ] Simd4FloatingpointTest.max (0 ms) 27: [ RUN ] Simd4FloatingpointTest.min 27: [ OK ] Simd4FloatingpointTest.min (0 ms) 27: [ RUN ] Simd4FloatingpointTest.round 27: [ OK ] Simd4FloatingpointTest.round (0 ms) 27: [ RUN ] Simd4FloatingpointTest.trunc 27: [ OK ] Simd4FloatingpointTest.trunc (0 ms) 27: [ RUN ] Simd4FloatingpointTest.gmxSimd4RsqrtR 27: [ OK ] Simd4FloatingpointTest.gmxSimd4RsqrtR (0 ms) 27: [ RUN ] Simd4FloatingpointTest.cmpEqAndSelectByMask 27: [ OK ] Simd4FloatingpointTest.cmpEqAndSelectByMask (0 ms) 27: [ RUN ] Simd4FloatingpointTest.selectByNotMask 27: [ OK ] Simd4FloatingpointTest.selectByNotMask (0 ms) 27: [ RUN ] Simd4FloatingpointTest.cmpNe 27: [ OK ] Simd4FloatingpointTest.cmpNe (0 ms) 27: [ RUN ] Simd4FloatingpointTest.cmpLe 27: [ OK ] Simd4FloatingpointTest.cmpLe (0 ms) 27: [ RUN ] Simd4FloatingpointTest.cmpLt 27: [ OK ] Simd4FloatingpointTest.cmpLt (0 ms) 27: [ RUN ] Simd4FloatingpointTest.andB 27: [ OK ] Simd4FloatingpointTest.andB (0 ms) 27: [ RUN ] Simd4FloatingpointTest.orB 27: [ OK ] Simd4FloatingpointTest.orB (0 ms) 27: [ RUN ] Simd4FloatingpointTest.anyTrue 27: [ OK ] Simd4FloatingpointTest.anyTrue (0 ms) 27: [ RUN ] Simd4FloatingpointTest.blend 27: [ OK ] Simd4FloatingpointTest.blend (0 ms) 27: [ RUN ] Simd4FloatingpointTest.reduce 27: [ OK ] Simd4FloatingpointTest.reduce (0 ms) 27: [ RUN ] Simd4FloatingpointTest.dotProduct 27: [ OK ] Simd4FloatingpointTest.dotProduct (0 ms) 27: [ RUN ] Simd4FloatingpointTest.transpose 27: [ OK ] Simd4FloatingpointTest.transpose (0 ms) 27: [----------] 32 tests from Simd4FloatingpointTest (1 ms total) 27: 27: [----------] 1 test from Simd4VectorOperationsTest 27: [ RUN ] Simd4VectorOperationsTest.norm2 27: [ OK ] Simd4VectorOperationsTest.norm2 (0 ms) 27: [----------] 1 test from Simd4VectorOperationsTest (0 ms total) 27: 27: [----------] 2 tests from Simd4MathTest 27: [ RUN ] Simd4MathTest.invsqrt 27: [ OK ] Simd4MathTest.invsqrt (0 ms) 27: [ RUN ] Simd4MathTest.invsqrtSingleAccuracy 27: [ OK ] Simd4MathTest.invsqrtSingleAccuracy (0 ms) 27: [----------] 2 tests from Simd4MathTest (0 ms total) 27: 27: [----------] 41 tests from SimdScalarTest 27: [ RUN ] SimdScalarTest.load 27: [ OK ] SimdScalarTest.load (0 ms) 27: [ RUN ] SimdScalarTest.loadU 27: [ OK ] SimdScalarTest.loadU (0 ms) 27: [ RUN ] SimdScalarTest.store 27: [ OK ] SimdScalarTest.store (0 ms) 27: [ RUN ] SimdScalarTest.storeU 27: [ OK ] SimdScalarTest.storeU (0 ms) 27: [ RUN ] SimdScalarTest.setZero 27: [ OK ] SimdScalarTest.setZero (0 ms) 27: [ RUN ] SimdScalarTest.andNot 27: [ OK ] SimdScalarTest.andNot (0 ms) 27: [ RUN ] SimdScalarTest.fma 27: [ OK ] SimdScalarTest.fma (0 ms) 27: [ RUN ] SimdScalarTest.fms 27: [ OK ] SimdScalarTest.fms (0 ms) 27: [ RUN ] SimdScalarTest.fnma 27: [ OK ] SimdScalarTest.fnma (0 ms) 27: [ RUN ] SimdScalarTest.fnms 27: [ OK ] SimdScalarTest.fnms (0 ms) 27: [ RUN ] SimdScalarTest.maskAdd 27: [ OK ] SimdScalarTest.maskAdd (0 ms) 27: [ RUN ] SimdScalarTest.maskzMul 27: [ OK ] SimdScalarTest.maskzMul (0 ms) 27: [ RUN ] SimdScalarTest.maskzFma 27: [ OK ] SimdScalarTest.maskzFma (0 ms) 27: [ RUN ] SimdScalarTest.abs 27: [ OK ] SimdScalarTest.abs (0 ms) 27: [ RUN ] SimdScalarTest.max 27: [ OK ] SimdScalarTest.max (0 ms) 27: [ RUN ] SimdScalarTest.min 27: [ OK ] SimdScalarTest.min (0 ms) 27: [ RUN ] SimdScalarTest.round 27: [ OK ] SimdScalarTest.round (0 ms) 27: [ RUN ] SimdScalarTest.trunc 27: [ OK ] SimdScalarTest.trunc (0 ms) 27: [ RUN ] SimdScalarTest.reduce 27: [ OK ] SimdScalarTest.reduce (0 ms) 27: [ RUN ] SimdScalarTest.testBits 27: [ OK ] SimdScalarTest.testBits (0 ms) 27: [ RUN ] SimdScalarTest.anyTrue 27: [ OK ] SimdScalarTest.anyTrue (0 ms) 27: [ RUN ] SimdScalarTest.selectByMask 27: [ OK ] SimdScalarTest.selectByMask (0 ms) 27: [ RUN ] SimdScalarTest.selectByNotMask 27: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 27: [ RUN ] SimdScalarTest.blend 27: [ OK ] SimdScalarTest.blend (0 ms) 27: [ RUN ] SimdScalarTest.cvtR2I 27: [ OK ] SimdScalarTest.cvtR2I (0 ms) 27: [ RUN ] SimdScalarTest.cvttR2I 27: [ OK ] SimdScalarTest.cvttR2I (0 ms) 27: [ RUN ] SimdScalarTest.cvtI2R 27: [ OK ] SimdScalarTest.cvtI2R (0 ms) 27: [ RUN ] SimdScalarTest.cvtF2D 27: [ OK ] SimdScalarTest.cvtF2D (0 ms) 27: [ RUN ] SimdScalarTest.cvtD2D 27: [ OK ] SimdScalarTest.cvtD2D (0 ms) 27: [ RUN ] SimdScalarTest.loadI 27: [ OK ] SimdScalarTest.loadI (0 ms) 27: [ RUN ] SimdScalarTest.loadUI 27: [ OK ] SimdScalarTest.loadUI (0 ms) 27: [ RUN ] SimdScalarTest.storeI 27: [ OK ] SimdScalarTest.storeI (0 ms) 27: [ RUN ] SimdScalarTest.storeUI 27: [ OK ] SimdScalarTest.storeUI (0 ms) 27: [ RUN ] SimdScalarTest.andNotI 27: [ OK ] SimdScalarTest.andNotI (0 ms) 27: [ RUN ] SimdScalarTest.testBitsI 27: [ OK ] SimdScalarTest.testBitsI (0 ms) 27: [ RUN ] SimdScalarTest.selectByMaskI 27: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 27: [ RUN ] SimdScalarTest.selectByNotMaskI 27: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 27: [ RUN ] SimdScalarTest.blendI 27: [ OK ] SimdScalarTest.blendI (0 ms) 27: [ RUN ] SimdScalarTest.cvtB2IB 27: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 27: [ RUN ] SimdScalarTest.cvtIB2B 27: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 27: [ RUN ] SimdScalarTest.expandScalarsToTriplets 27: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 27: [----------] 41 tests from SimdScalarTest (0 ms total) 27: 27: [----------] 8 tests from SimdScalarUtilTest 27: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 27: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 27: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 27: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 27: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 27: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 27: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 27: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 27: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 27: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 27: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 27: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 27: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 27: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 27: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 27: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 27: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 27: 27: [----------] 37 tests from SimdScalarMathTest 27: [ RUN ] SimdScalarMathTest.copysign 27: [ OK ] SimdScalarMathTest.copysign (0 ms) 27: [ RUN ] SimdScalarMathTest.invsqrtPair 27: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 27: [ RUN ] SimdScalarMathTest.inv 27: [ OK ] SimdScalarMathTest.inv (0 ms) 27: [ RUN ] SimdScalarMathTest.maskzInvsqrt 27: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 27: [ RUN ] SimdScalarMathTest.log 27: [ OK ] SimdScalarMathTest.log (0 ms) 27: [ RUN ] SimdScalarMathTest.exp2 27: [ OK ] SimdScalarMathTest.exp2 (0 ms) 27: [ RUN ] SimdScalarMathTest.exp 27: [ OK ] SimdScalarMathTest.exp (0 ms) 27: [ RUN ] SimdScalarMathTest.erf 27: [ OK ] SimdScalarMathTest.erf (0 ms) 27: [ RUN ] SimdScalarMathTest.erfc 27: [ OK ] SimdScalarMathTest.erfc (0 ms) 27: [ RUN ] SimdScalarMathTest.sincos 27: [ OK ] SimdScalarMathTest.sincos (0 ms) 27: [ RUN ] SimdScalarMathTest.sin 27: [ OK ] SimdScalarMathTest.sin (0 ms) 27: [ RUN ] SimdScalarMathTest.cos 27: [ OK ] SimdScalarMathTest.cos (0 ms) 27: [ RUN ] SimdScalarMathTest.tan 27: [ OK ] SimdScalarMathTest.tan (0 ms) 27: [ RUN ] SimdScalarMathTest.asin 27: [ OK ] SimdScalarMathTest.asin (0 ms) 27: [ RUN ] SimdScalarMathTest.acos 27: [ OK ] SimdScalarMathTest.acos (0 ms) 27: [ RUN ] SimdScalarMathTest.atan 27: [ OK ] SimdScalarMathTest.atan (0 ms) 27: [ RUN ] SimdScalarMathTest.atan2 27: [ OK ] SimdScalarMathTest.atan2 (0 ms) 27: [ RUN ] SimdScalarMathTest.pmeForceCorrection 27: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 27: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 27: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 27: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 27: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.invSingleAccuracy 27: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 27: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.logSingleAccuracy 27: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 27: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.expSingleAccuracy 27: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 27: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 27: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 27: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 27: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 27: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 27: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 27: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 27: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 27: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 27: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 27: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 27: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 27: [----------] 37 tests from SimdScalarMathTest (0 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 288 tests from 22 test cases ran. (65 ms total) 27: [ PASSED ] 288 tests. 27/54 Test #27: SimdUnitTests ....................... Passed 0.08 sec test 28 Start 28: CompatibilityHelpersTests 28: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/compat-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/CompatibilityHelpersTests.xml" 28: Test timeout computed to be: 30 28: [==========] Running 170 tests from 12 test cases. 28: [----------] Global test environment set-up. 28: [----------] 45 tests from OptionalTest 28: [ RUN ] OptionalTest.UnionCanContainNonPodTypes 28: [ OK ] OptionalTest.UnionCanContainNonPodTypes (0 ms) 28: [ RUN ] OptionalTest.CanDefaultConstructEmpty 28: [ OK ] OptionalTest.CanDefaultConstructEmpty (0 ms) 28: [ RUN ] OptionalTest.CanConstructFromNullopt 28: [ OK ] OptionalTest.CanConstructFromNullopt (0 ms) 28: [ RUN ] OptionalTest.CanDefaultConstructUsingNonDefaultConstructibleType 28: [ OK ] OptionalTest.CanDefaultConstructUsingNonDefaultConstructibleType (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptional 28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptional (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptional 28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptional (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptionalWithExplicitConversion 28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptionalWithExplicitConversion (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptionalNonExplicitConverting 28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptionalNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptionalExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptionalExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptionalNonExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptionalNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptional 28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptional (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptionalExplicitConverting 28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptionalExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptionalNonExplicitConverting 28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptionalNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptional 28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptional (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptionalExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptionalExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptionalNonExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptionalNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromLiteral 28: [ OK ] OptionalTest.CanCopyConstructFromLiteral (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromLiteralConverting 28: [ OK ] OptionalTest.CanCopyConstructFromLiteralConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromValue 28: [ OK ] OptionalTest.CanCopyConstructFromValue (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromValueConverting 28: [ OK ] OptionalTest.CanCopyConstructFromValueConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromValue 28: [ OK ] OptionalTest.CanMoveConstructFromValue (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromValueExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromValueExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromValueNonExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromValueNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceConstructFromLiteral 28: [ OK ] OptionalTest.CanInPlaceConstructFromLiteral (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceCopyConstructFromValue 28: [ OK ] OptionalTest.CanInPlaceCopyConstructFromValue (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceMoveConstructFromValue 28: [ OK ] OptionalTest.CanInPlaceMoveConstructFromValue (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceCopyConstructFromInitializerList 28: [ OK ] OptionalTest.CanInPlaceCopyConstructFromInitializerList (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceMoveConstructFromInitializerList 28: [ OK ] OptionalTest.CanInPlaceMoveConstructFromInitializerList (0 ms) 28: [ RUN ] OptionalTest.CanAssignNulloptToDisengage 28: [ OK ] OptionalTest.CanAssignNulloptToDisengage (0 ms) 28: [ RUN ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionals 28: [ OK ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionals (0 ms) 28: [ RUN ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionalsConverting 28: [ OK ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionalsConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionalsConverting 28: [ OK ] OptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionalsConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyAssignFromLiteral 28: [ OK ] OptionalTest.CanCopyAssignFromLiteral (0 ms) 28: [ RUN ] OptionalTest.CanCopyAssignFromValue 28: [ OK ] OptionalTest.CanCopyAssignFromValue (0 ms) 28: [ RUN ] OptionalTest.CanMoveAssignFromValue 28: [ OK ] OptionalTest.CanMoveAssignFromValue (0 ms) 28: [ RUN ] OptionalTest.CanCopyEmplaceFromArguments 28: [ OK ] OptionalTest.CanCopyEmplaceFromArguments (0 ms) 28: [ RUN ] OptionalTest.CanMoveEmplaceFromArguments 28: [ OK ] OptionalTest.CanMoveEmplaceFromArguments (0 ms) 28: [ RUN ] OptionalTest.CanCopyEmplaceFromInitializerListAndArguments 28: [ OK ] OptionalTest.CanCopyEmplaceFromInitializerListAndArguments (0 ms) 28: [ RUN ] OptionalTest.CanMoveEmplaceFromInitializerListAndArguments 28: [ OK ] OptionalTest.CanMoveEmplaceFromInitializerListAndArguments (0 ms) 28: [ RUN ] OptionalTest.CanResetContent 28: [ OK ] OptionalTest.CanResetContent (0 ms) 28: [ RUN ] OptionalTest.ProvidesRelationalOperators 28: [ OK ] OptionalTest.ProvidesRelationalOperators (0 ms) 28: [ RUN ] OptionalTest.ProvidesMixedTypeRelationalOperators 28: [ OK ] OptionalTest.ProvidesMixedTypeRelationalOperators (0 ms) 28: [ RUN ] OptionalTest.CanProduceHash 28: [ OK ] OptionalTest.CanProduceHash (0 ms) 28: [ RUN ] OptionalTest.ShowAlignmentDependingOnBaseType 28: alignment_of: 1 28: alignment_of: 2 28: alignment_of: 4 28: alignment_of: 8 28: alignment_of: 4 28: alignment_of: 8 28: alignment_of: 16 28: alignment_of: 1 28: [ OK ] OptionalTest.ShowAlignmentDependingOnBaseType (0 ms) 28: [ RUN ] OptionalTest.ShowSizeDependingOnBaseType 28: sizeof( nonstd::optional_lite::detail::storage_t ): 1 28: sizeof( optional ): 2 (1) 28: sizeof( optional ): 4 (2) 28: sizeof( optional ): 8 (4) 28: sizeof( optional ): 16 (8) 28: sizeof( optional ): 8 (4) 28: sizeof( optional ): 16 (8) 28: sizeof( optional ): 32 (16) 28: sizeof( optional ): 2 (1) 28: [ OK ] OptionalTest.ShowSizeDependingOnBaseType (0 ms) 28: [----------] 45 tests from OptionalTest (1 ms total) 28: 28: [----------] 7 tests from MakeOptionalTest 28: [ RUN ] MakeOptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionals 28: [ OK ] MakeOptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionals (0 ms) 28: [ RUN ] MakeOptionalTest.CanCopyConstruct 28: [ OK ] MakeOptionalTest.CanCopyConstruct (0 ms) 28: [ RUN ] MakeOptionalTest.CanMoveConstruct 28: [ OK ] MakeOptionalTest.CanMoveConstruct (0 ms) 28: [ RUN ] MakeOptionalTest.CanInPlaceCopyConstructFromArguments 28: [ OK ] MakeOptionalTest.CanInPlaceCopyConstructFromArguments (0 ms) 28: [ RUN ] MakeOptionalTest.CanInPlaceMoveConstructFromArguments 28: [ OK ] MakeOptionalTest.CanInPlaceMoveConstructFromArguments (0 ms) 28: [ RUN ] MakeOptionalTest.CanInPlaceCopyConstructFromInitializerListAndArguments 28: [ OK ] MakeOptionalTest.CanInPlaceCopyConstructFromInitializerListAndArguments (0 ms) 28: [ RUN ] MakeOptionalTest.CanInPlaceMoveConstructFromInitializerListAndArguments 28: [ OK ] MakeOptionalTest.CanInPlaceMoveConstructFromInitializerListAndArguments (0 ms) 28: [----------] 7 tests from MakeOptionalTest (0 ms total) 28: 28: [----------] 4 tests from OptionalMemberSwapTest 28: [ RUN ] OptionalMemberSwapTest.CanSwapDisengagedWithDisengaged 28: [ OK ] OptionalMemberSwapTest.CanSwapDisengagedWithDisengaged (0 ms) 28: [ RUN ] OptionalMemberSwapTest.CanSwapEngagedWithDisengaged 28: [ OK ] OptionalMemberSwapTest.CanSwapEngagedWithDisengaged (0 ms) 28: [ RUN ] OptionalMemberSwapTest.CanSwapDisengagedWithEngaged 28: [ OK ] OptionalMemberSwapTest.CanSwapDisengagedWithEngaged (0 ms) 28: [ RUN ] OptionalMemberSwapTest.CanSwapEngagedWithEngaged 28: [ OK ] OptionalMemberSwapTest.CanSwapEngagedWithEngaged (0 ms) 28: [----------] 4 tests from OptionalMemberSwapTest (0 ms total) 28: 28: [----------] 4 tests from OptionalImplicitValueTest 28: [ RUN ] OptionalImplicitValueTest.CanObtainValueConst 28: [ OK ] OptionalImplicitValueTest.CanObtainValueConst (0 ms) 28: [ RUN ] OptionalImplicitValueTest.CanObtainValueNonConst 28: [ OK ] OptionalImplicitValueTest.CanObtainValueNonConst (0 ms) 28: [ RUN ] OptionalImplicitValueTest.CanObtainMovedFromValueConst 28: [ OK ] OptionalImplicitValueTest.CanObtainMovedFromValueConst (0 ms) 28: [ RUN ] OptionalImplicitValueTest.CanObtainMovedFromValueNonConst 28: [ OK ] OptionalImplicitValueTest.CanObtainMovedFromValueNonConst (0 ms) 28: [----------] 4 tests from OptionalImplicitValueTest (0 ms total) 28: 28: [----------] 20 tests from OptionalIntValueTest 28: [ RUN ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorConst 28: [ OK ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorNonConst 28: [ OK ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorNonConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorConst 28: [ OK ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorNonConst 28: [ OK ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorNonConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainHasValueViaOperatorBool 28: [ OK ] OptionalIntValueTest.CanObtainHasValueViaOperatorBool (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainValueViaValueMethodConst 28: [ OK ] OptionalIntValueTest.CanObtainValueViaValueMethodConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainValueViaValueMethodNonConst 28: [ OK ] OptionalIntValueTest.CanObtainValueViaValueMethodNonConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodConst 28: [ OK ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodNonConst 28: [ OK ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodNonConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainValueFromNonEmptyOptionalViaValueOrMethod 28: [ OK ] OptionalIntValueTest.CanObtainValueFromNonEmptyOptionalViaValueOrMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainDefaultFromEmptyOptionalViaValueOrMethod 28: [ OK ] OptionalIntValueTest.CanObtainDefaultFromEmptyOptionalViaValueOrMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedFromValueForLValuesViaValueOrMethod 28: [ OK ] OptionalIntValueTest.CanObtainMovedFromValueForLValuesViaValueOrMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedFromValueForRValuesViaValueOrMethod 28: [ OK ] OptionalIntValueTest.CanObtainMovedFromValueForRValuesViaValueOrMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForLValues 28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForLValues (0 ms) 28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForRValues 28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForRValues (0 ms) 28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessWithNonEmptyWhatMethod 28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessWithNonEmptyWhatMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithDisengaged 28: [ OK ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithDisengaged (0 ms) 28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithEngaged 28: [ OK ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithEngaged (0 ms) 28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithEngaged 28: [ OK ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithEngaged (0 ms) 28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithDisengaged 28: [ OK ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithDisengaged (0 ms) 28: [----------] 20 tests from OptionalIntValueTest (0 ms total) 28: 28: [----------] 1 test from NotNullConstruction 28: [ RUN ] NotNullConstruction.Works 28: [ OK ] NotNullConstruction.Works (0 ms) 28: [----------] 1 test from NotNullConstruction (0 ms total) 28: 28: [----------] 1 test from NotNullCasting 28: [ RUN ] NotNullCasting.Works 28: [ OK ] NotNullCasting.Works (0 ms) 28: [----------] 1 test from NotNullCasting (0 ms total) 28: 28: [----------] 1 test from NotNullAssignment 28: [ RUN ] NotNullAssignment.Works 28: [ OK ] NotNullAssignment.Works (0 ms) 28: [----------] 1 test from NotNullAssignment (0 ms total) 28: 28: [----------] 1 test from MakeNotNull 28: [ RUN ] MakeNotNull.Works 28: [ OK ] MakeNotNull.Works (0 ms) 28: [----------] 1 test from MakeNotNull (0 ms total) 28: 28: [----------] 1 test from NotNull 28: [ RUN ] NotNull.WorksInContainers 28: [ OK ] NotNull.WorksInContainers (0 ms) 28: [----------] 1 test from NotNull (0 ms total) 28: 28: [----------] 80 tests from StringViewTest 28: [ RUN ] StringViewTest.CanDefaultConstructEmptyView 28: [ OK ] StringViewTest.CanDefaultConstructEmptyView (0 ms) 28: [ RUN ] StringViewTest.CanConstructFromPointerAndSize 28: [ OK ] StringViewTest.CanConstructFromPointerAndSize (0 ms) 28: [ RUN ] StringViewTest.CanConstructFromCString 28: [ OK ] StringViewTest.CanConstructFromCString (0 ms) 28: [ RUN ] StringViewTest.CanCopyConstructFromEmptyView 28: [ OK ] StringViewTest.CanCopyConstructFromEmptyView (0 ms) 28: [ RUN ] StringViewTest.CanCopyConstructFromNonEmptyView 28: [ OK ] StringViewTest.CanCopyConstructFromNonEmptyView (0 ms) 28: [ RUN ] StringViewTest.CanCopyAssingFromEmptyView 28: [ OK ] StringViewTest.CanCopyAssingFromEmptyView (0 ms) 28: [ RUN ] StringViewTest.CanCopyAssingFromNonEmptyView 28: [ OK ] StringViewTest.CanCopyAssingFromNonEmptyView (0 ms) 28: [ RUN ] StringViewTest.AllowForwardIteration 28: [ OK ] StringViewTest.AllowForwardIteration (0 ms) 28: [ RUN ] StringViewTest.AllowConstForwardIteration 28: [ OK ] StringViewTest.AllowConstForwardIteration (0 ms) 28: [ RUN ] StringViewTest.AllowReverseIteration 28: [ OK ] StringViewTest.AllowReverseIteration (0 ms) 28: [ RUN ] StringViewTest.AllowConstReverseIteration 28: [ OK ] StringViewTest.AllowConstReverseIteration (0 ms) 28: [ RUN ] StringViewTest.CanObtainSizeFromViewViaSize 28: [ OK ] StringViewTest.CanObtainSizeFromViewViaSize (0 ms) 28: [ RUN ] StringViewTest.CanObtainSizeFromViewViaLength 28: [ OK ] StringViewTest.CanObtainSizeFromViewViaLength (0 ms) 28: [ RUN ] StringViewTest.CanObtainMaxSizeViaMaxSize 28: [ OK ] StringViewTest.CanObtainMaxSizeViaMaxSize (1 ms) 28: [ RUN ] StringViewTest.CanCheckForEmptyStringWithEmpty 28: [ OK ] StringViewTest.CanCheckForEmptyStringWithEmpty (0 ms) 28: [ RUN ] StringViewTest.CanAccessElementViaArrayIndex 28: [ OK ] StringViewTest.CanAccessElementViaArrayIndex (0 ms) 28: [ RUN ] StringViewTest.CanAccessElementViaAt 28: [ OK ] StringViewTest.CanAccessElementViaAt (0 ms) 28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsAccess 28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsAccess (0 ms) 28: [ RUN ] StringViewTest.CanAccessAllElementsViaData 28: [ OK ] StringViewTest.CanAccessAllElementsViaData (0 ms) 28: [ RUN ] StringViewTest.DataFromEmptyStringIsNullptr 28: [ OK ] StringViewTest.DataFromEmptyStringIsNullptr (0 ms) 28: [ RUN ] StringViewTest.CanRemovePrefix 28: [ OK ] StringViewTest.CanRemovePrefix (0 ms) 28: [ RUN ] StringViewTest.CanRemoveSuffix 28: [ OK ] StringViewTest.CanRemoveSuffix (0 ms) 28: [ RUN ] StringViewTest.CanSwapWithOtherView 28: [ OK ] StringViewTest.CanSwapWithOtherView (0 ms) 28: [ RUN ] StringViewTest.CanCopySubstringWithCopy 28: [ OK ] StringViewTest.CanCopySubstringWithCopy (0 ms) 28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsCopy 28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsCopy (0 ms) 28: [ RUN ] StringViewTest.CanObtainSubstringWithSubstr 28: [ OK ] StringViewTest.CanObtainSubstringWithSubstr (0 ms) 28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsSubstr 28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsSubstr (0 ms) 28: [ RUN ] StringViewTest.CanLexicallyCompareViewWithCompare 28: [ OK ] StringViewTest.CanLexicallyCompareViewWithCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareEmptyViewsWIthCompare 28: [ OK ] StringViewTest.CanCompareEmptyViewsWIthCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareSubStringWithViewViaCompare 28: [ OK ] StringViewTest.CanCompareSubStringWithViewViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareSubStringWithSubStringViewViaCompare 28: [ OK ] StringViewTest.CanCompareSubStringWithSubStringViewViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareToCStringViaCompare 28: [ OK ] StringViewTest.CanCompareToCStringViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareSubStringToCStringViaCompare 28: [ OK ] StringViewTest.CanCompareSubStringToCStringViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareSubStringToCStringPrefixViaCompare 28: [ OK ] StringViewTest.CanCompareSubStringToCStringPrefixViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCheckForPrefixViewViaStartsWith 28: [ OK ] StringViewTest.CanCheckForPrefixViewViaStartsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForPrefixCharacterViaStartsWith 28: [ OK ] StringViewTest.CanCheckForPrefixCharacterViaStartsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForPrefixCStringViaStartsWith 28: [ OK ] StringViewTest.CanCheckForPrefixCStringViaStartsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForSuffixViewViaEndsWith 28: [ OK ] StringViewTest.CanCheckForSuffixViewViaEndsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForSuffixCharacterViaEndsWith 28: [ OK ] StringViewTest.CanCheckForSuffixCharacterViaEndsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForSuffixCStringViaEndsWith 28: [ OK ] StringViewTest.CanCheckForSuffixCStringViaEndsWith (0 ms) 28: [ RUN ] StringViewTest.CanSearchForViewSubstrViaFind 28: [ OK ] StringViewTest.CanSearchForViewSubstrViaFind (0 ms) 28: [ RUN ] StringViewTest.CanSearchForCharacterViaFind 28: [ OK ] StringViewTest.CanSearchForCharacterViaFind (0 ms) 28: [ RUN ] StringViewTest.CanSearchForCStringSubstringViaFind 28: [ OK ] StringViewTest.CanSearchForCStringSubstringViaFind (0 ms) 28: [ RUN ] StringViewTest.CanSearchForCStringSubstringViaFindWithDefaultPos 28: [ OK ] StringViewTest.CanSearchForCStringSubstringViaFindWithDefaultPos (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForViewSubstrViaFind 28: [ OK ] StringViewTest.CanBackwardsSearchForViewSubstrViaFind (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForCharacterViaFind 28: [ OK ] StringViewTest.CanBackwardsSearchForCharacterViaFind (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFind 28: [ OK ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFind (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFindWithDefaultPos 28: [ OK ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFindWithDefaultPos (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfAnyCharacterInView 28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfAnyCharacterInView (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharacter 28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharacter (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCStringInLenght 28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCStringInLenght (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCString 28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCString (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfAnyCharacterInView 28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfAnyCharacterInView (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharacter 28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharacter (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCStringInLenght 28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCStringInLenght (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCString 28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCString (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstNotFoundCharacter 28: [ OK ] StringViewTest.CanSearchForFirstNotFoundCharacter (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstNonMatchingCharacter 28: [ OK ] StringViewTest.CanSearchForFirstNonMatchingCharacter (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCStringInLength 28: [ OK ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCStringInLength (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCString 28: [ OK ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCString (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForForstNonFoundCharacterInView 28: [ OK ] StringViewTest.CanBackwardsSearchForForstNonFoundCharacterInView (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonMatchingCharacter 28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonMatchingCharacter (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCStringInLength 28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCStringInLength (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCString 28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCString (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSV 28: [ OK ] StringViewTest.CanCreateViewWithLiteralSV (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsStringViewLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsStringViewLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInStringViewLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInStringViewLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SV 28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SV (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsStringViewLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsStringViewLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInStringViewLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInStringViewLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCompareToViews 28: [ OK ] StringViewTest.CanCompareToViews (0 ms) 28: [ RUN ] StringViewTest.CanCompareViewToImplicitlyConvertedView 28: [ OK ] StringViewTest.CanCompareViewToImplicitlyConvertedView (0 ms) 28: [ RUN ] StringViewTest.EmptyViewsCompareAsEqual 28: [ OK ] StringViewTest.EmptyViewsCompareAsEqual (0 ms) 28: [ RUN ] StringViewTest.CanPrintViewToPutputStream 28: [ OK ] StringViewTest.CanPrintViewToPutputStream (0 ms) 28: [ RUN ] StringViewTest.HashOfViewIsEqualToHashOfString 28: [ OK ] StringViewTest.HashOfViewIsEqualToHashOfString (0 ms) 28: [ RUN ] StringViewTest.HashOfWStringViewIsEqualToHashOfString 28: [ OK ] StringViewTest.HashOfWStringViewIsEqualToHashOfString (0 ms) 28: [ RUN ] StringViewTest.HashOfU16StringViewIsEqualToHashOfString 28: [ OK ] StringViewTest.HashOfU16StringViewIsEqualToHashOfString (1 ms) 28: [ RUN ] StringViewTest.HashOfU32StringViewIsEqualToHashOfString 28: [ OK ] StringViewTest.HashOfU32StringViewIsEqualToHashOfString (0 ms) 28: [----------] 80 tests from StringViewTest (2 ms total) 28: 28: [----------] 5 tests from StringViewExtensionTest 28: [ RUN ] StringViewExtensionTest.CanConstructViewFromString 28: [ OK ] StringViewExtensionTest.CanConstructViewFromString (0 ms) 28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaExplicitOperator 28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaExplicitOperator (0 ms) 28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaToString 28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaToString (0 ms) 28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaToStringFreeFunction 28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaToStringFreeFunction (0 ms) 28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViewViaToStringView 28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViewViaToStringView (0 ms) 28: [----------] 5 tests from StringViewExtensionTest (0 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 170 tests from 12 test cases ran. (3 ms total) 28: [ PASSED ] 170 tests. 28/54 Test #28: CompatibilityHelpersTests ........... Passed 0.02 sec test 29 Start 29: GmxAnaTest 29: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/gmxana-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/GmxAnaTest.xml" 29: Test timeout computed to be: 600 29: [==========] Running 27 tests from 5 test cases. 29: [----------] Global test environment set-up. 29: [----------] 5 tests from Entropy 29: [ RUN ] Entropy.Schlitter_300_NoLinear 29: [ OK ] Entropy.Schlitter_300_NoLinear (0 ms) 29: [ RUN ] Entropy.Schlitter_300_Linear 29: [ OK ] Entropy.Schlitter_300_Linear (0 ms) 29: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear 29: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms) 29: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear 29: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms) 29: [ RUN ] Entropy.QuasiHarmonic_200_Linear 29: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms) 29: [----------] 5 tests from Entropy (0 ms total) 29: 29: [----------] 10 tests from MindistTest 29: [ RUN ] MindistTest.mindistWorksWithSingleAtoms 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 0: 'atom1' 29: Selected 1: 'atom2' 29: [ OK ] MindistTest.mindistWorksWithSingleAtoms (57 ms) 29: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 2: 'atom3' 29: Selected 3: 'atoms12' 29: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (2 ms) 29: [ RUN ] MindistTest.mindistDoesNotPickUpContacts 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 0: 'atom1' 29: Selected 1: 'atom2' 29: [ OK ] MindistTest.mindistDoesNotPickUpContacts (2 ms) 29: [ RUN ] MindistTest.mindistPicksUpContacts 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 0: 'atom1' 29: Selected 1: 'atom2' 29: [ OK ] MindistTest.mindistPicksUpContacts (3 ms) 29: [ RUN ] MindistTest.ngWorks 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 0: 'atom1' 29: Selected 1: 'atom2' 29: Selected 2: 'atom3' 29: [ OK ] MindistTest.ngWorks (2 ms) 29: [ RUN ] MindistTest.groupWorks 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 3: 'atoms12' 29: Selected 2: 'atom3' 29: [ OK ] MindistTest.groupWorks (2 ms) 29: [ RUN ] MindistTest.maxDistWorks 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 2: 'atom3' 29: Selected 3: 'atoms12' 29: [ OK ] MindistTest.maxDistWorks (2 ms) 29: [ RUN ] MindistTest.noPbcWorks 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 0: 'atom1' 29: Selected 1: 'atom2' 29: [ OK ] MindistTest.noPbcWorks (1 ms) 29: [ RUN ] MindistTest.resPerTimeWorks 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 3: 'atoms12' 29: Selected 2: 'atom3' 29: [ OK ] MindistTest.resPerTimeWorks (1 ms) 29: [ RUN ] MindistTest.matrixWorks 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 5: 'atoms123' 29: Special case: making distance matrix between all atoms in group atoms123 29: [ OK ] MindistTest.matrixWorks (1 ms) 29: [----------] 10 tests from MindistTest (73 ms total) 29: 29: [----------] 3 tests from MsdTest 29: [ RUN ] MsdTest.threeDimensionalDiffusion 29: 29: Select a group to calculate mean squared displacement for: 29: Group 0 ( particles) has 3 elements 29: There is one group in the index 29: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 29: 29: Used 1 restart points spaced 200 ps over 9 ps 29: 29: Fitting from 1 to 8 ps 29: 29: D[ particles] 4.0000 (+/- 0.0000) 1e-5 cm^2/s 29: [ OK ] MsdTest.threeDimensionalDiffusion (1 ms) 29: [ RUN ] MsdTest.twoDimensionalDiffusion 29: 29: Select a group to calculate mean squared displacement for: 29: Group 0 ( particles) has 3 elements 29: There is one group in the index 29: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 29: 29: Used 1 restart points spaced 200 ps over 9 ps 29: 29: Fitting from 1 to 8 ps 29: 29: D[ particles] 6.0000 (+/- 0.0000) 1e-5 cm^2/s 29: [ OK ] MsdTest.twoDimensionalDiffusion (1 ms) 29: [ RUN ] MsdTest.oneDimensionalDiffusion 29: 29: Select a group to calculate mean squared displacement for: 29: Group 0 ( particles) has 3 elements 29: There is one group in the index 29: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 29: 29: Used 1 restart points spaced 200 ps over 9 ps 29: 29: Fitting from 1 to 8 ps 29: 29: D[ particles] 8.0000 (+/- 0.0000) 1e-5 cm^2/s 29: [ OK ] MsdTest.oneDimensionalDiffusion (0 ms) 29: [----------] 3 tests from MsdTest (3 ms total) 29: 29: [----------] 3 tests from MsdMolTest 29: [ RUN ] MsdMolTest.diffMolMassWeighted 29: 29: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]: 29: For a correct single-point energy evaluation with nsteps = 0, use 29: continuation = yes to avoid constraining the input coordinates. 29: 29: Setting the LD random seed to -575144235 29: Generated 330891 of the 330891 non-bonded parameter combinations 29: Generating 1-4 interactions: fudge = 0.5 29: Generated 330891 of the 330891 1-4 parameter combinations 29: Excluding 2 bonded neighbours molecule type 'SOL' 29: Number of degrees of freedom in T-Coupling group rest is 27.00 29: 29: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]: 29: NVE simulation with an initial temperature of zero: will use a Verlet 29: buffer of 10%. Check your energy drift! 29: 29: 29: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]: 29: You are using a plain Coulomb cut-off, which might produce artifacts. 29: You might want to consider using PME electrostatics. 29: 29: 29: 29: There were 3 notes 29: Calculating diffusion coefficients for molecules. 29: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 29: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 29: 29: Select a group to calculate mean squared displacement for: 29: Group 0 ( water) has 15 elements 29: There is one group in the index 29: Split group of 15 atoms into 5 molecules 29: Reading frames from pdb file Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms 29: Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Reading frame 5 time 0.020 Reading frame 6 time 0.024 Reading frame 7 time 0.028 Reading frame 8 time 0.032 Reading frame 9 time 0.036 Reading frame 10 time 0.040 Reading frame 11 time 0.044 Reading frame 12 time 0.048 Reading frame 13 time 0.052 Reading frame 14 time 0.056 Reading frame 15 time 0.060 Reading frame 16 time 0.064 Reading frame 17 time 0.068 Reading frame 18 time 0.072 Reading frame 19 time 0.076 Reading frame 20 time 0.080 29: 29: Used 1 restart points spaced 200 ps over 0.1 ps 29: 29: This run will generate roughly 0 Mb of data 29: = 6.4731 Std. Dev. = 8.0969 Error = 3.6210 29: Fitting from 0.008 to 0.088 ps 29: 29: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s 29: [ OK ] MsdMolTest.diffMolMassWeighted (1068 ms) 29: [ RUN ] MsdMolTest.diffMolNonMassWeighted 29: 29: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]: 29: For a correct single-point energy evaluation with nsteps = 0, use 29: continuation = yes to avoid constraining the input coordinates. 29: 29: Setting the LD random seed to -589185034 29: Generated 330891 of the 330891 non-bonded parameter combinations 29: Generating 1-4 interactions: fudge = 0.5 29: Generated 330891 of the 330891 1-4 parameter combinations 29: Excluding 2 bonded neighbours molecule type 'SOL' 29: Number of degrees of freedom in T-Coupling group rest is 27.00 29: 29: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]: 29: NVE simulation with an initial temperature of zero: will use a Verlet 29: buffer of 10%. Check your energy drift! 29: 29: 29: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]: 29: You are using a plain Coulomb cut-off, which might produce artifacts. 29: You might want to consider using PME electrostatics. 29: 29: 29: 29: There were 3 notes 29: Calculating diffusion coefficients for molecules. 29: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 29: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 29: 29: Select a group to calculate mean squared displacement for: 29: Group 0 ( water) has 15 elements 29: There is one group in the index 29: Split group of 15 atoms into 5 molecules 29: Reading frames from pdb file Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms 29: Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Reading frame 5 time 0.020 Reading frame 6 time 0.024 Reading frame 7 time 0.028 Reading frame 8 time 0.032 Reading frame 9 time 0.036 Reading frame 10 time 0.040 Reading frame 11 time 0.044 Reading frame 12 time 0.048 Reading frame 13 time 0.052 Reading frame 14 time 0.056 Reading frame 15 time 0.060 Reading frame 16 time 0.064 Reading frame 17 time 0.068 Reading frame 18 time 0.072 Reading frame 19 time 0.076 Reading frame 20 time 0.080 29: 29: Used 1 restart points spaced 200 ps over 0.1 ps 29: 29: This run will generate roughly 0 Mb of data 29: = 6.4731 Std. Dev. = 8.0969 Error = 3.6210 29: Fitting from 0.008 to 0.088 ps 29: 29: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s 29: [ OK ] MsdMolTest.diffMolNonMassWeighted (441 ms) 29: [ RUN ] MsdMolTest.diffMolSelected 29: 29: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]: 29: For a correct single-point energy evaluation with nsteps = 0, use 29: continuation = yes to avoid constraining the input coordinates. 29: 29: Setting the LD random seed to 1970723807 29: Generated 330891 of the 330891 non-bonded parameter combinations 29: Generating 1-4 interactions: fudge = 0.5 29: Generated 330891 of the 330891 1-4 parameter combinations 29: Excluding 2 bonded neighbours molecule type 'SOL' 29: Number of degrees of freedom in T-Coupling group rest is 27.00 29: 29: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]: 29: NVE simulation with an initial temperature of zero: will use a Verlet 29: buffer of 10%. Check your energy drift! 29: 29: 29: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]: 29: You are using a plain Coulomb cut-off, which might produce artifacts. 29: You might want to consider using PME electrostatics. 29: 29: 29: 29: There were 3 notes 29: Calculating diffusion coefficients for molecules. 29: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 29: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 29: 29: Select a group to calculate mean squared displacement for: 29: Group 0 ( mol) has 9 elements 29: There is one group in the index 29: Split group of 9 atoms into 3 molecules 29: Reading frames from pdb file Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms 29: Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Reading frame 5 time 0.020 Reading frame 6 time 0.024 Reading frame 7 time 0.028 Reading frame 8 time 0.032 Reading frame 9 time 0.036 Reading frame 10 time 0.040 Reading frame 11 time 0.044 Reading frame 12 time 0.048 Reading frame 13 time 0.052 Reading frame 14 time 0.056 Reading frame 15 time 0.060 Reading frame 16 time 0.064 Reading frame 17 time 0.068 Reading frame 18 time 0.072 Reading frame 19 time 0.076 Reading frame 20 time 0.080 29: 29: Used 1 restart points spaced 200 ps over 0.1 ps 29: 29: This run will generate roughly 0 Mb of data 29: = 7.3593 Std. Dev. = 9.7910 Error = 5.6529 29: Fitting from 0.008 to 0.088 ps 29: 29: D[ mol] 7.8614 (+/- 1.5618) 1e-5 cm^2/s 29: [ OK ] MsdMolTest.diffMolSelected (501 ms) 29: [----------] 3 tests from MsdMolTest (2010 ms total) 29: 29: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj 29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 29: Group 0 ( System) has 6 elements 29: Group 1 ( Water) has 6 elements 29: Group 2 ( SOL) has 6 elements 29: Select a group: trr version: GMX_trn_file (single precision) 29: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 29: Selected 0: 'System' 29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (1 ms) 29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 29: Group 0 ( System) has 6 elements 29: Group 1 ( Water) has 6 elements 29: Group 2 ( SOL) has 6 elements 29: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 29: Selected 0: 'System' 29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (2 ms) 29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 29: Group 0 ( System) has 6 elements 29: Group 1 ( Water) has 6 elements 29: Group 2 ( SOL) has 6 elements 29: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 29: Selected 0: 'System' 29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (2 ms) 29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 29: Group 0 ( System) has 6 elements 29: Group 1 ( Water) has 6 elements 29: Group 2 ( SOL) has 6 elements 29: Select a group: Reading frames from gro file '', 6 atoms. 29: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 29: Selected 0: 'System' 29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (2 ms) 29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 29: Group 0 ( System) has 6 elements 29: Group 1 ( Water) has 6 elements 29: Group 2 ( SOL) has 6 elements 29: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 't= 0.00000', 6 atoms 29: Reading frame 1 time 0.000 Last frame 1 time 0.000 29: Selected 0: 'System' 29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (1 ms) 29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 29: Group 0 ( System) has 6 elements 29: Group 1 ( Water) has 6 elements 29: Group 2 ( SOL) has 6 elements 29: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 29: Selected 0: 'System' 29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (2 ms) 29: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj (10 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 27 tests from 5 test cases ran. (2097 ms total) 29: [ PASSED ] 27 tests. 29/54 Test #29: GmxAnaTest .......................... Passed 2.11 sec test 30 Start 30: GmxPreprocessTests 30: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/gmxpreprocess-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/GmxPreprocessTests.xml" 30: Test timeout computed to be: 30 30: [==========] Running 69 tests from 10 test cases. 30: [----------] Global test environment set-up. 30: [----------] 4 tests from GenconfTest 30: [ RUN ] GenconfTest.nbox_Works 30: [ OK ] GenconfTest.nbox_Works (1 ms) 30: [ RUN ] GenconfTest.nbox_norenumber_Works 30: [ OK ] GenconfTest.nbox_norenumber_Works (0 ms) 30: [ RUN ] GenconfTest.nbox_dist_Works 30: [ OK ] GenconfTest.nbox_dist_Works (1 ms) 30: [ RUN ] GenconfTest.nbox_rot_Works 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: [ OK ] GenconfTest.nbox_rot_Works (1 ms) 30: [----------] 4 tests from GenconfTest (3 ms total) 30: 30: [----------] 2 tests from GenionTest 30: [ RUN ] GenionTest.HighConcentrationIonPlacement 30: 30: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 30: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 30: buffer. The cluster pair list does have a buffering effect, but choosing 30: a larger rlist might be necessary for good energy conservation. 30: 30: 30: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: Setting the LD random seed to -34213905 30: Generated 331705 of the 331705 non-bonded parameter combinations 30: Generating 1-4 interactions: fudge = 0.5 30: Generated 331705 of the 331705 1-4 parameter combinations 30: Excluding 2 bonded neighbours molecule type 'SOL' 30: Excluding 3 bonded neighbours molecule type 'methane' 30: Number of degrees of freedom in T-Coupling group rest is 1308.00 30: 30: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 30: You are using a plain Coulomb cut-off, which might produce artifacts. 30: You might want to consider using PME electrostatics. 30: 30: 30: 30: There were 3 notes 30: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 30: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 30: Group 0 ( System) has 653 elements 30: Group 1 ( Water) has 648 elements 30: Group 2 ( SOL) has 648 elements 30: Group 3 ( non-Water) has 5 elements 30: Group 4 ( Other) has 5 elements 30: Group 5 ( METH) has 5 elements 30: Select a group: Number of (3-atomic) solvent molecules: 216 30: Using random seed 1997. 30: Replacing solvent molecule 56 (atom 168) with NA 30: Replacing solvent molecule 120 (atom 360) with NA 30: Replacing solvent molecule 182 (atom 546) with NA 30: Replacing solvent molecule 71 (atom 213) with NA 30: Replacing solvent molecule 189 (atom 567) with CL 30: Replacing solvent molecule 54 (atom 162) with CL 30: Replacing solvent molecule 155 (atom 465) with CL 30: Replacing solvent molecule 99 (atom 297) with CL 30: 30: Analysing residue names: 30: There are: 216 Water residues 30: There are: 1 Other residues 30: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 30: This run will generate roughly 0 Mb of data 30: Will try to add 4 NA ions and 4 CL ions. 30: Select a continuous group of solvent molecules 30: Selected 1: 'Water' 30: [ OK ] GenionTest.HighConcentrationIonPlacement (687 ms) 30: [ RUN ] GenionTest.NoIonPlacement 30: 30: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 30: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 30: buffer. The cluster pair list does have a buffering effect, but choosing 30: a larger rlist might be necessary for good energy conservation. 30: 30: 30: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: Setting the LD random seed to -169390137 30: Generated 331705 of the 331705 non-bonded parameter combinations 30: Generating 1-4 interactions: fudge = 0.5 30: Generated 331705 of the 331705 1-4 parameter combinations 30: Excluding 2 bonded neighbours molecule type 'SOL' 30: Excluding 3 bonded neighbours molecule type 'methane' 30: Number of degrees of freedom in T-Coupling group rest is 1308.00 30: 30: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 30: You are using a plain Coulomb cut-off, which might produce artifacts. 30: You might want to consider using PME electrostatics. 30: 30: 30: 30: There were 3 notes 30: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 30: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 30: No ions to add, will just copy input configuration. 30: Analysing residue names: 30: There are: 216 Water residues 30: There are: 1 Other residues 30: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 30: This run will generate roughly 0 Mb of data 30: [ OK ] GenionTest.NoIonPlacement (453 ms) 30: [----------] 2 tests from GenionTest (1140 ms total) 30: 30: [----------] 1 test from GenRestrTest 30: [ RUN ] GenRestrTest.SimpleRestraintsGenerated 30: 30: Reading structure file 30: Group 0 ( System) has 156 elements 30: Group 1 ( Protein) has 156 elements 30: Group 2 ( Protein-H) has 75 elements 30: Group 3 ( C-alpha) has 10 elements 30: Group 4 ( Backbone) has 30 elements 30: Group 5 ( MainChain) has 40 elements 30: Group 6 ( MainChain+Cb) has 49 elements 30: Group 7 ( MainChain+H) has 52 elements 30: Group 8 ( SideChain) has 104 elements 30: Group 9 ( SideChain-H) has 35 elements 30: Select a group: Select group to position restrain 30: Selected 3: 'C-alpha' 30: [ OK ] GenRestrTest.SimpleRestraintsGenerated (4 ms) 30: [----------] 1 test from GenRestrTest (4 ms total) 30: 30: [----------] 9 tests from PreprocessingAtomTypesTest 30: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate 30: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms) 30: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid 30: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms) 30: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks 30: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms) 30: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks 30: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms) 30: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry 30: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms) 30: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound 30: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms) 30: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound 30: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms) 30: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber 30: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms) 30: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber 30: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms) 30: [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total) 30: 30: [----------] 10 tests from PreprocessingBondAtomTypeTest 30: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate 30: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms) 30: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid 30: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms) 30: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks 30: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms) 30: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks 30: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms) 30: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry 30: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms) 30: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType 30: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms) 30: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound 30: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms) 30: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound 30: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms) 30: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber 30: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms) 30: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber 30: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (1 ms) 30: [----------] 10 tests from PreprocessingBondAtomTypeTest (1 ms total) 30: 30: [----------] 5 tests from InsertMoleculesTest 30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration 30: Reading solute configuration 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Using random seed 1997 30: Try 1 success (now 8 atoms)! 30: 30: Added 1 molecules (out of 1 requested) 30: Writing generated configuration to /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro 30: 30: Output configuration contains 8 atoms in 4 residues 30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (2 ms) 30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Using random seed 1997 30: Try 1 success (now 2 atoms)! 30: Try 2 success (now 4 atoms)! 30: Try 3 success (now 6 atoms)! 30: Try 4 success (now 8 atoms)! 30: Try 5 success (now 10 atoms)! 30: 30: Added 5 molecules (out of 5 requested) 30: Writing generated configuration to /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro 30: 30: Output configuration contains 10 atoms in 10 residues 30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (1 ms) 30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox 30: Reading solute configuration 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Using random seed 1997 30: Try 1 success (now 8 atoms)! 30: Try 2 success (now 10 atoms)! 30: 30: Added 2 molecules (out of 2 requested) 30: Writing generated configuration to /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro 30: 30: Output configuration contains 10 atoms in 4 residues 30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (2 ms) 30: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement 30: Reading solute configuration 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Using random seed 1997 30: Try 1 success (now 650 atoms)! 30: Try 2 success (now 652 atoms)! 30: Try 3 success (now 654 atoms)! 30: Try 4 success (now 656 atoms)! 30: 30: Added 4 molecules (out of 4 requested) 30: Replaced 8 residues (24 atoms) 30: Writing generated configuration to /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro 30: 30: Output configuration contains 632 atoms in 212 residues 30: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (6 ms) 30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Using random seed 1997 30: Read 4 positions from file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat 30: 30: Try 1 success (now 2 atoms)! 30: Try 2 success (now 4 atoms)! 30: Try 3 Try 4 Try 5 Try 6 Try 7 Try 8 Try 9 Try 10 Try 11 Try 12 skipped position (0.990, 2.010, 3.000) 30: Try 13 success (now 6 atoms)! 30: 30: Added 3 molecules (out of 4 requested) 30: Writing generated configuration to /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro 30: 30: Output configuration contains 6 atoms in 3 residues 30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (2 ms) 30: [----------] 5 tests from InsertMoleculesTest (13 ms total) 30: 30: [----------] 14 tests from GetIrTest 30: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines 30: Ignoring obsolete mdp entry 'title' 30: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' 30: 30: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (4 ms) 30: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals 30: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (6 ms) 30: [ RUN ] GetIrTest.AcceptsKeyWithoutValue 30: 30: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: [ OK ] GetIrTest.AcceptsKeyWithoutValue (3 ms) 30: [ RUN ] GetIrTest.RejectsValueWithoutKey 30: [ OK ] GetIrTest.RejectsValueWithoutKey (5 ms) 30: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue 30: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (5 ms) 30: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment 30: 30: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (2 ms) 30: [ RUN ] GetIrTest.AcceptsEmptyLines 30: 30: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: [ OK ] GetIrTest.AcceptsEmptyLines (3 ms) 30: [ RUN ] GetIrTest.AcceptsElectricField 30: 30: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: [ OK ] GetIrTest.AcceptsElectricField (3 ms) 30: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed 30: 30: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (3 ms) 30: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating 30: 30: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (3 ms) 30: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys 30: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (2 ms) 30: [ RUN ] GetIrTest.AcceptsImplicitSolventNo 30: 30: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: [ OK ] GetIrTest.AcceptsImplicitSolventNo (3 ms) 30: [ RUN ] GetIrTest.RejectsImplicitSolventYes 30: [ OK ] GetIrTest.RejectsImplicitSolventYes (4 ms) 30: [ RUN ] GetIrTest.AcceptsMimic 30: 30: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: [ OK ] GetIrTest.AcceptsMimic (3 ms) 30: [----------] 14 tests from GetIrTest (49 ms total) 30: 30: [----------] 5 tests from SolvateTest 30: [ RUN ] SolvateTest.cs_box_Works 30: Reading solvent configuration 30: 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Generating solvent configuration 30: Will generate new solvent configuration of 1x1x1 boxes 30: Solvent box contains 270 atoms in 90 residues 30: Removed 129 solvent atoms due to solvent-solvent overlap 30: Sorting configuration 30: Found 1 molecule type: 30: SOL ( 3 atoms): 47 residues 30: Generated solvent containing 141 atoms in 47 residues 30: Writing generated configuration to /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro 30: 30: Output configuration contains 141 atoms in 47 residues 30: Volume : 1.331 (nm^3) 30: Density : 1056.36 (g/l) 30: Number of solvent molecules: 47 30: 30: [ OK ] SolvateTest.cs_box_Works (7 ms) 30: [ RUN ] SolvateTest.cs_cp_Works 30: Reading solute configuration 30: Reading solvent configuration 30: 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Generating solvent configuration 30: Will generate new solvent configuration of 2x2x2 boxes 30: Solvent box contains 3660 atoms in 1220 residues 30: Removed 987 solvent atoms due to solvent-solvent overlap 30: Removed 15 solvent atoms due to solute-solvent overlap 30: Sorting configuration 30: Found 1 molecule type: 30: SOL ( 3 atoms): 886 residues 30: Generated solvent containing 2658 atoms in 886 residues 30: Writing generated configuration to /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro 30: 30: Output configuration contains 2664 atoms in 888 residues 30: Volume : 27.2709 (nm^3) 30: Density : 974.777 (g/l) 30: Number of solvent molecules: 886 30: 30: [ OK ] SolvateTest.cs_cp_Works (70 ms) 30: [ RUN ] SolvateTest.cs_cp_p_Works 30: Reading solute configuration 30: Reading solvent configuration 30: 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Generating solvent configuration 30: Will generate new solvent configuration of 2x2x2 boxes 30: Solvent box contains 3660 atoms in 1220 residues 30: Removed 987 solvent atoms due to solvent-solvent overlap 30: Removed 15 solvent atoms due to solute-solvent overlap 30: Sorting configuration 30: Found 1 molecule type: 30: SOL ( 3 atoms): 886 residues 30: Generated solvent containing 2658 atoms in 886 residues 30: Writing generated configuration to /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro 30: 30: Output configuration contains 2664 atoms in 888 residues 30: Volume : 27.2709 (nm^3) 30: Density : 974.777 (g/l) 30: Number of solvent molecules: 886 30: 30: Processing topology 30: Adding line for 886 solvent molecules with resname (SOL) to topology file (/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top) 30: [ OK ] SolvateTest.cs_cp_p_Works (61 ms) 30: [ RUN ] SolvateTest.shell_Works 30: Reading solute configuration 30: Reading solvent configuration 30: 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Generating solvent configuration 30: Will generate new solvent configuration of 2x2x2 boxes 30: Solvent box contains 3660 atoms in 1220 residues 30: Removed 987 solvent atoms due to solvent-solvent overlap 30: Removed 1902 solvent atoms more than 1.000000 nm from solute. 30: Removed 15 solvent atoms due to solute-solvent overlap 30: Sorting configuration 30: Found 1 molecule type: 30: SOL ( 3 atoms): 252 residues 30: Generated solvent containing 756 atoms in 252 residues 30: Writing generated configuration to /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro 30: 30: Output configuration contains 762 atoms in 254 residues 30: Volume : 27.2709 (nm^3) 30: Density : 279.3 (g/l) 30: Number of solvent molecules: 252 30: 30: [ OK ] SolvateTest.shell_Works (28 ms) 30: [ RUN ] SolvateTest.update_Topology_Works 30: Reading solute configuration 30: Reading solvent configuration 30: 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Generating solvent configuration 30: Will generate new solvent configuration of 3x3x3 boxes 30: Solvent box contains 14952 atoms in 4984 residues 30: Removed 2787 solvent atoms due to solvent-solvent overlap 30: Removed 30 solvent atoms due to solute-solvent overlap 30: Sorting configuration 30: Found 2 different molecule types: 30: HOH ( 3 atoms): 1876 residues 30: SOL ( 3 atoms): 2169 residues 30: Generated solvent containing 0 atoms in 0 residues 30: Writing generated configuration to /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro 30: 30: Output configuration contains 12141 atoms in 4047 residues 30: Volume : 125 (nm^3) 30: Density : 968.963 (g/l) 30: Number of solvent molecules: 4045 30: 30: Processing topology 30: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 30: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 30: [ OK ] SolvateTest.update_Topology_Works (233 ms) 30: [----------] 5 tests from SolvateTest (399 ms total) 30: 30: [----------] 1 test from TopDirTests 30: [ RUN ] TopDirTests.NamesArrayHasCorrectSize 30: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms) 30: [----------] 1 test from TopDirTests (0 ms total) 30: 30: [----------] 18 tests from SinglePeptideFragments/EditconfTest 30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 30: Note that major changes are planned in future for editconf, to improve usability and utility. 30: Read 252 atoms 30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 30: No velocities found 30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 (6 ms) 30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 30: Note that major changes are planned in future for editconf, to improve usability and utility. 30: Read 252 atoms 30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 30: No velocities found 30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 (30 ms) 30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 30: Note that major changes are planned in future for editconf, to improve usability and utility. 30: Read 252 atoms 30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 30: No velocities found 30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 (7 ms) 30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 30: Note that major changes are planned in future for editconf, to improve usability and utility. 30: Read 252 atoms 30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 30: No velocities found 30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 (3 ms) 30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 30: Note that major changes are planned in future for editconf, to improve usability and utility. 30: Read 252 atoms 30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 30: No velocities found 30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 (2 ms) 30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 30: Note that major changes are planned in future for editconf, to improve usability and utility. 30: Read 252 atoms 30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 30: No velocities found 30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 (3 ms) 30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 30: Note that major changes are planned in future for editconf, to improve usability and utility. 30: Read 252 atoms 30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 30: No velocities found 30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 (3 ms) 30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 30: Note that major changes are planned in future for editconf, to improve usability and utility. 30: Read 252 atoms 30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 30: No velocities found 30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 (2 ms) 30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 30: Note that major changes are planned in future for editconf, to improve usability and utility. 30: Read 252 atoms 30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 30: No velocities found 30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 (2 ms) 30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 30: 30: Select a group for output: 30: Group 0 ( two_residues) has 23 elements 30: There is one group in the index 30: Note that major changes are planned in future for editconf, to improve usability and utility. 30: Read 252 atoms 30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 30: No velocities found 30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 (4 ms) 30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 30: 30: Select a group for output: 30: Group 0 ( two_residues) has 23 elements 30: There is one group in the index 30: Note that major changes are planned in future for editconf, to improve usability and utility. 30: Read 252 atoms 30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 30: No velocities found 30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 (4 ms) 30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 30: 30: Select a group for output: 30: Group 0 ( two_residues) has 23 elements 30: There is one group in the index 30: Note that major changes are planned in future for editconf, to improve usability and utility. 30: Read 252 atoms 30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 30: No velocities found 30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 (4 ms) 30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 30: 30: Select a group for output: 30: Group 0 ( two_residues) has 23 elements 30: There is one group in the index 30: Note that major changes are planned in future for editconf, to improve usability and utility. 30: Read 252 atoms 30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 30: No velocities found 30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 (2 ms) 30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 30: 30: Select a group for output: 30: Group 0 ( two_residues) has 23 elements 30: There is one group in the index 30: Note that major changes are planned in future for editconf, to improve usability and utility. 30: Read 252 atoms 30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 30: No velocities found 30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 (1 ms) 30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 30: 30: Select a group for output: 30: Group 0 ( two_residues) has 23 elements 30: There is one group in the index 30: Note that major changes are planned in future for editconf, to improve usability and utility. 30: Read 252 atoms 30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 30: No velocities found 30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 (2 ms) 30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 30: 30: Select a group for output: 30: Group 0 ( two_residues) has 23 elements 30: There is one group in the index 30: Note that major changes are planned in future for editconf, to improve usability and utility. 30: Read 252 atoms 30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 30: No velocities found 30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 (2 ms) 30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 30: 30: Select a group for output: 30: Group 0 ( two_residues) has 23 elements 30: There is one group in the index 30: Note that major changes are planned in future for editconf, to improve usability and utility. 30: Read 252 atoms 30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 30: No velocities found 30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 (1 ms) 30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 30: 30: Select a group for output: 30: Group 0 ( two_residues) has 23 elements 30: There is one group in the index 30: Note that major changes are planned in future for editconf, to improve usability and utility. 30: Read 252 atoms 30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 30: No velocities found 30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 (2 ms) 30: [----------] 18 tests from SinglePeptideFragments/EditconfTest (80 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 69 tests from 10 test cases ran. (1689 ms total) 30: [ PASSED ] 69 tests. 30/54 Test #30: GmxPreprocessTests .................. Passed 1.70 sec test 31 Start 31: Pdb2gmx1Test 31: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/pdb2gmx1-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/Pdb2gmx1Test.xml" 31: Test timeout computed to be: 30 31: [==========] Running 24 tests from 1 test case. 31: [----------] Global test environment set-up. 31: [----------] 24 tests from ForOplsaa/Pdb2gmxTest 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 25 donors and 23 acceptors were found. 31: There are 41 hydrogen bonds 31: Will use HISE for residue 8 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS3 HIS8 31: SG9 NE251 31: HIS8 NE251 1.055 31: MET12 SD83 0.763 0.990 31: Making bonds... 31: Number of bonds was 254, now 254 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 653 pairs 31: Before cleaning: 663 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 663 dihedrals, 51 impropers, 457 angles 31: 650 pairs, 254 bonds and 0 virtual sites 31: Total mass 1846.112 a.m.u. 31: Total charge -0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 128 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (128 atoms, 16 residues) 31: Identified residue ALA2 as a starting terminus. 31: Identified residue SER17 as a ending terminus. 31: Start terminus ALA-2: NH3+ 31: End terminus SER-17: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 252 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 31: The Oplsaa force field and the tip3p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0 (89 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 30 donors and 22 acceptors were found. 31: There are 36 hydrogen bonds 31: Will use HISE for residue 29 31: Will use HISE for residue 32 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS27 HIS29 31: SG90 NE2111 31: HIS29 NE2111 0.987 31: HIS32 NE2135 1.590 1.155 31: Making bonds... 31: Number of bonds was 290, now 290 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 748 pairs 31: Before cleaning: 778 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 778 dihedrals, 72 impropers, 516 angles 31: 736 pairs, 290 bonds and 0 virtual sites 31: Total mass 2088.357 a.m.u. 31: Total charge 1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 149 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (149 atoms, 16 residues) 31: Identified residue THR18 as a starting terminus. 31: Identified residue PHE33 as a ending terminus. 31: Start terminus THR-18: NH3+ 31: End terminus PHE-33: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 281 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 31: The Oplsaa force field and the tip3p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1 (151 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 22 acceptors were found. 31: There are 26 hydrogen bonds 31: Will use HISE for residue 45 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS45 31: NE295 31: MET46 SD102 1.078 31: Making bonds... 31: Number of bonds was 261, now 261 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 676 pairs 31: Before cleaning: 696 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 696 dihedrals, 56 impropers, 472 angles 31: 667 pairs, 261 bonds and 0 virtual sites 31: Total mass 1861.128 a.m.u. 31: Total charge -1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 132 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (132 atoms, 16 residues) 31: Identified residue ALA34 as a starting terminus. 31: Identified residue ALA49 as a ending terminus. 31: Start terminus ALA-34: NH3+ 31: End terminus ALA-49: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 255 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 31: The Oplsaa force field and the tip3p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2 (104 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 21 acceptors were found. 31: There are 30 hydrogen bonds 31: Will use HISE for residue 60 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS60 31: NE285 31: CYS62 SG98 0.803 31: Making bonds... 31: Number of bonds was 232, now 232 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 603 pairs 31: Before cleaning: 618 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 618 dihedrals, 48 impropers, 419 angles 31: 597 pairs, 232 bonds and 0 virtual sites 31: Total mass 1662.883 a.m.u. 31: Total charge -0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 117 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (117 atoms, 16 residues) 31: Identified residue LYS50 as a starting terminus. 31: Identified residue PRO65 as a ending terminus. 31: Start terminus LYS-50: NH3+ 31: End terminus PRO-65: PRO-COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 228 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 31: The Oplsaa force field and the tip3p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3 (62 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 25 donors and 23 acceptors were found. 31: There are 41 hydrogen bonds 31: Will use HISE for residue 8 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS3 HIS8 31: SG9 NE251 31: HIS8 NE251 1.055 31: MET12 SD83 0.763 0.990 31: Making bonds... 31: Number of bonds was 254, now 254 31: Marked 124 virtual sites 31: Added 16 dummy masses 31: Added 26 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 653 pairs 31: Before cleaning: 663 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 663 dihedrals, 51 impropers, 457 angles 31: 650 pairs, 254 bonds and 130 virtual sites 31: Total mass 1846.112 a.m.u. 31: Total charge -0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 128 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (128 atoms, 16 residues) 31: Identified residue ALA2 as a starting terminus. 31: Identified residue SER17 as a ending terminus. 31: Start terminus ALA-2: NH3+ 31: End terminus SER-17: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 252 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 31: The Oplsaa force field and the tip3p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4 (159 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 30 donors and 22 acceptors were found. 31: There are 36 hydrogen bonds 31: Will use HISE for residue 29 31: Will use HISE for residue 32 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS27 HIS29 31: SG90 NE2111 31: HIS29 NE2111 0.987 31: HIS32 NE2135 1.590 1.155 31: Making bonds... 31: Number of bonds was 290, now 290 31: Marked 132 virtual sites 31: Added 10 dummy masses 31: Added 19 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 748 pairs 31: Before cleaning: 778 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 778 dihedrals, 72 impropers, 516 angles 31: 736 pairs, 290 bonds and 133 virtual sites 31: Total mass 2088.357 a.m.u. 31: Total charge 1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 149 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (149 atoms, 16 residues) 31: Identified residue THR18 as a starting terminus. 31: Identified residue PHE33 as a ending terminus. 31: Start terminus THR-18: NH3+ 31: End terminus PHE-33: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 281 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 31: The Oplsaa force field and the tip3p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5 (117 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 22 acceptors were found. 31: There are 26 hydrogen bonds 31: Will use HISE for residue 45 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS45 31: NE295 31: MET46 SD102 1.078 31: Making bonds... 31: Number of bonds was 261, now 261 31: Marked 123 virtual sites 31: Added 22 dummy masses 31: Added 35 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 676 pairs 31: Before cleaning: 696 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 696 dihedrals, 56 impropers, 472 angles 31: 667 pairs, 261 bonds and 132 virtual sites 31: Total mass 1861.128 a.m.u. 31: Total charge -1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 132 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (132 atoms, 16 residues) 31: Identified residue ALA34 as a starting terminus. 31: Identified residue ALA49 as a ending terminus. 31: Start terminus ALA-34: NH3+ 31: End terminus ALA-49: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 255 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 31: The Oplsaa force field and the tip3p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6 (158 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 21 acceptors were found. 31: There are 30 hydrogen bonds 31: Will use HISE for residue 60 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS60 31: NE285 31: CYS62 SG98 0.803 31: Making bonds... 31: Number of bonds was 232, now 232 31: Marked 111 virtual sites 31: Added 18 dummy masses 31: Added 31 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 603 pairs 31: Before cleaning: 618 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 618 dihedrals, 48 impropers, 419 angles 31: 597 pairs, 232 bonds and 116 virtual sites 31: Total mass 1662.883 a.m.u. 31: Total charge -0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 117 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (117 atoms, 16 residues) 31: Identified residue LYS50 as a starting terminus. 31: Identified residue PRO65 as a ending terminus. 31: Start terminus LYS-50: NH3+ 31: End terminus PRO-65: PRO-COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 228 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 31: The Oplsaa force field and the tip3p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7 (160 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 25 donors and 23 acceptors were found. 31: There are 41 hydrogen bonds 31: Will use HISE for residue 8 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS3 HIS8 31: SG9 NE251 31: HIS8 NE251 1.055 31: MET12 SD83 0.763 0.990 31: Making bonds... 31: Number of bonds was 254, now 254 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 653 pairs 31: Before cleaning: 663 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 663 dihedrals, 51 impropers, 457 angles 31: 650 pairs, 254 bonds and 0 virtual sites 31: Total mass 1846.112 a.m.u. 31: Total charge -0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 128 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (128 atoms, 16 residues) 31: Identified residue ALA2 as a starting terminus. 31: Identified residue SER17 as a ending terminus. 31: Start terminus ALA-2: NH3+ 31: End terminus SER-17: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 252 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 31: The Oplsaa force field and the tip4p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8 (107 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 30 donors and 22 acceptors were found. 31: There are 36 hydrogen bonds 31: Will use HISE for residue 29 31: Will use HISE for residue 32 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS27 HIS29 31: SG90 NE2111 31: HIS29 NE2111 0.987 31: HIS32 NE2135 1.590 1.155 31: Making bonds... 31: Number of bonds was 290, now 290 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 748 pairs 31: Before cleaning: 778 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 778 dihedrals, 72 impropers, 516 angles 31: 736 pairs, 290 bonds and 0 virtual sites 31: Total mass 2088.357 a.m.u. 31: Total charge 1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 149 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (149 atoms, 16 residues) 31: Identified residue THR18 as a starting terminus. 31: Identified residue PHE33 as a ending terminus. 31: Start terminus THR-18: NH3+ 31: End terminus PHE-33: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 281 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 31: The Oplsaa force field and the tip4p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9 (146 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 22 acceptors were found. 31: There are 26 hydrogen bonds 31: Will use HISE for residue 45 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS45 31: NE295 31: MET46 SD102 1.078 31: Making bonds... 31: Number of bonds was 261, now 261 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 676 pairs 31: Before cleaning: 696 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 696 dihedrals, 56 impropers, 472 angles 31: 667 pairs, 261 bonds and 0 virtual sites 31: Total mass 1861.128 a.m.u. 31: Total charge -1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 132 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (132 atoms, 16 residues) 31: Identified residue ALA34 as a starting terminus. 31: Identified residue ALA49 as a ending terminus. 31: Start terminus ALA-34: NH3+ 31: End terminus ALA-49: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 255 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 31: The Oplsaa force field and the tip4p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10 (135 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 21 acceptors were found. 31: There are 30 hydrogen bonds 31: Will use HISE for residue 60 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS60 31: NE285 31: CYS62 SG98 0.803 31: Making bonds... 31: Number of bonds was 232, now 232 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 603 pairs 31: Before cleaning: 618 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 618 dihedrals, 48 impropers, 419 angles 31: 597 pairs, 232 bonds and 0 virtual sites 31: Total mass 1662.883 a.m.u. 31: Total charge -0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 117 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (117 atoms, 16 residues) 31: Identified residue LYS50 as a starting terminus. 31: Identified residue PRO65 as a ending terminus. 31: Start terminus LYS-50: NH3+ 31: End terminus PRO-65: PRO-COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 228 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 31: The Oplsaa force field and the tip4p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11 (96 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 25 donors and 23 acceptors were found. 31: There are 41 hydrogen bonds 31: Will use HISE for residue 8 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS3 HIS8 31: SG9 NE251 31: HIS8 NE251 1.055 31: MET12 SD83 0.763 0.990 31: Making bonds... 31: Number of bonds was 254, now 254 31: Marked 124 virtual sites 31: Added 16 dummy masses 31: Added 26 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 653 pairs 31: Before cleaning: 663 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 663 dihedrals, 51 impropers, 457 angles 31: 650 pairs, 254 bonds and 130 virtual sites 31: Total mass 1846.112 a.m.u. 31: Total charge -0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 128 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (128 atoms, 16 residues) 31: Identified residue ALA2 as a starting terminus. 31: Identified residue SER17 as a ending terminus. 31: Start terminus ALA-2: NH3+ 31: End terminus SER-17: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 252 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 31: The Oplsaa force field and the tip4p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12 (135 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 30 donors and 22 acceptors were found. 31: There are 36 hydrogen bonds 31: Will use HISE for residue 29 31: Will use HISE for residue 32 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS27 HIS29 31: SG90 NE2111 31: HIS29 NE2111 0.987 31: HIS32 NE2135 1.590 1.155 31: Making bonds... 31: Number of bonds was 290, now 290 31: Marked 132 virtual sites 31: Added 10 dummy masses 31: Added 19 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 748 pairs 31: Before cleaning: 778 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 778 dihedrals, 72 impropers, 516 angles 31: 736 pairs, 290 bonds and 133 virtual sites 31: Total mass 2088.357 a.m.u. 31: Total charge 1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 149 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (149 atoms, 16 residues) 31: Identified residue THR18 as a starting terminus. 31: Identified residue PHE33 as a ending terminus. 31: Start terminus THR-18: NH3+ 31: End terminus PHE-33: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 281 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 31: The Oplsaa force field and the tip4p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13 (156 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 22 acceptors were found. 31: There are 26 hydrogen bonds 31: Will use HISE for residue 45 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS45 31: NE295 31: MET46 SD102 1.078 31: Making bonds... 31: Number of bonds was 261, now 261 31: Marked 123 virtual sites 31: Added 22 dummy masses 31: Added 35 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 676 pairs 31: Before cleaning: 696 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 696 dihedrals, 56 impropers, 472 angles 31: 667 pairs, 261 bonds and 132 virtual sites 31: Total mass 1861.128 a.m.u. 31: Total charge -1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 132 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (132 atoms, 16 residues) 31: Identified residue ALA34 as a starting terminus. 31: Identified residue ALA49 as a ending terminus. 31: Start terminus ALA-34: NH3+ 31: End terminus ALA-49: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 255 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 31: The Oplsaa force field and the tip4p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14 (130 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 21 acceptors were found. 31: There are 30 hydrogen bonds 31: Will use HISE for residue 60 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS60 31: NE285 31: CYS62 SG98 0.803 31: Making bonds... 31: Number of bonds was 232, now 232 31: Marked 111 virtual sites 31: Added 18 dummy masses 31: Added 31 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 603 pairs 31: Before cleaning: 618 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 618 dihedrals, 48 impropers, 419 angles 31: 597 pairs, 232 bonds and 116 virtual sites 31: Total mass 1662.883 a.m.u. 31: Total charge -0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 117 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (117 atoms, 16 residues) 31: Identified residue LYS50 as a starting terminus. 31: Identified residue PRO65 as a ending terminus. 31: Start terminus LYS-50: NH3+ 31: End terminus PRO-65: PRO-COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 228 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 31: The Oplsaa force field and the tip4p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15 (90 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 25 donors and 23 acceptors were found. 31: There are 41 hydrogen bonds 31: Will use HISE for residue 8 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS3 HIS8 31: SG9 NE251 31: HIS8 NE251 1.055 31: MET12 SD83 0.763 0.990 31: Making bonds... 31: Number of bonds was 254, now 254 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 653 pairs 31: Before cleaning: 663 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 663 dihedrals, 51 impropers, 457 angles 31: 650 pairs, 254 bonds and 0 virtual sites 31: Total mass 1846.112 a.m.u. 31: Total charge -0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 128 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (128 atoms, 16 residues) 31: Identified residue ALA2 as a starting terminus. 31: Identified residue SER17 as a ending terminus. 31: Start terminus ALA-2: NH3+ 31: End terminus SER-17: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 252 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 31: The Oplsaa force field and the tip5p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16 (90 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 30 donors and 22 acceptors were found. 31: There are 36 hydrogen bonds 31: Will use HISE for residue 29 31: Will use HISE for residue 32 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS27 HIS29 31: SG90 NE2111 31: HIS29 NE2111 0.987 31: HIS32 NE2135 1.590 1.155 31: Making bonds... 31: Number of bonds was 290, now 290 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 748 pairs 31: Before cleaning: 778 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 778 dihedrals, 72 impropers, 516 angles 31: 736 pairs, 290 bonds and 0 virtual sites 31: Total mass 2088.357 a.m.u. 31: Total charge 1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 149 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (149 atoms, 16 residues) 31: Identified residue THR18 as a starting terminus. 31: Identified residue PHE33 as a ending terminus. 31: Start terminus THR-18: NH3+ 31: End terminus PHE-33: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 281 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 31: The Oplsaa force field and the tip5p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17 (96 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 22 acceptors were found. 31: There are 26 hydrogen bonds 31: Will use HISE for residue 45 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS45 31: NE295 31: MET46 SD102 1.078 31: Making bonds... 31: Number of bonds was 261, now 261 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 676 pairs 31: Before cleaning: 696 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 696 dihedrals, 56 impropers, 472 angles 31: 667 pairs, 261 bonds and 0 virtual sites 31: Total mass 1861.128 a.m.u. 31: Total charge -1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 132 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (132 atoms, 16 residues) 31: Identified residue ALA34 as a starting terminus. 31: Identified residue ALA49 as a ending terminus. 31: Start terminus ALA-34: NH3+ 31: End terminus ALA-49: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 255 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 31: The Oplsaa force field and the tip5p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18 (103 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 21 acceptors were found. 31: There are 30 hydrogen bonds 31: Will use HISE for residue 60 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS60 31: NE285 31: CYS62 SG98 0.803 31: Making bonds... 31: Number of bonds was 232, now 232 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 603 pairs 31: Before cleaning: 618 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 618 dihedrals, 48 impropers, 419 angles 31: 597 pairs, 232 bonds and 0 virtual sites 31: Total mass 1662.883 a.m.u. 31: Total charge -0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 117 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (117 atoms, 16 residues) 31: Identified residue LYS50 as a starting terminus. 31: Identified residue PRO65 as a ending terminus. 31: Start terminus LYS-50: NH3+ 31: End terminus PRO-65: PRO-COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 228 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 31: The Oplsaa force field and the tip5p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19 (80 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 25 donors and 23 acceptors were found. 31: There are 41 hydrogen bonds 31: Will use HISE for residue 8 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS3 HIS8 31: SG9 NE251 31: HIS8 NE251 1.055 31: MET12 SD83 0.763 0.990 31: Making bonds... 31: Number of bonds was 254, now 254 31: Marked 124 virtual sites 31: Added 16 dummy masses 31: Added 26 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 653 pairs 31: Before cleaning: 663 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 663 dihedrals, 51 impropers, 457 angles 31: 650 pairs, 254 bonds and 130 virtual sites 31: Total mass 1846.112 a.m.u. 31: Total charge -0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 128 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (128 atoms, 16 residues) 31: Identified residue ALA2 as a starting terminus. 31: Identified residue SER17 as a ending terminus. 31: Start terminus ALA-2: NH3+ 31: End terminus SER-17: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 252 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 31: The Oplsaa force field and the tip5p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20 (124 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 30 donors and 22 acceptors were found. 31: There are 36 hydrogen bonds 31: Will use HISE for residue 29 31: Will use HISE for residue 32 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS27 HIS29 31: SG90 NE2111 31: HIS29 NE2111 0.987 31: HIS32 NE2135 1.590 1.155 31: Making bonds... 31: Number of bonds was 290, now 290 31: Marked 132 virtual sites 31: Added 10 dummy masses 31: Added 19 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 748 pairs 31: Before cleaning: 778 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 778 dihedrals, 72 impropers, 516 angles 31: 736 pairs, 290 bonds and 133 virtual sites 31: Total mass 2088.357 a.m.u. 31: Total charge 1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 149 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (149 atoms, 16 residues) 31: Identified residue THR18 as a starting terminus. 31: Identified residue PHE33 as a ending terminus. 31: Start terminus THR-18: NH3+ 31: End terminus PHE-33: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 281 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 31: The Oplsaa force field and the tip5p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21 (126 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 22 acceptors were found. 31: There are 26 hydrogen bonds 31: Will use HISE for residue 45 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS45 31: NE295 31: MET46 SD102 1.078 31: Making bonds... 31: Number of bonds was 261, now 261 31: Marked 123 virtual sites 31: Added 22 dummy masses 31: Added 35 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 676 pairs 31: Before cleaning: 696 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 696 dihedrals, 56 impropers, 472 angles 31: 667 pairs, 261 bonds and 132 virtual sites 31: Total mass 1861.128 a.m.u. 31: Total charge -1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 132 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (132 atoms, 16 residues) 31: Identified residue ALA34 as a starting terminus. 31: Identified residue ALA49 as a ending terminus. 31: Start terminus ALA-34: NH3+ 31: End terminus ALA-49: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 255 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 31: The Oplsaa force field and the tip5p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22 (156 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 21 acceptors were found. 31: There are 30 hydrogen bonds 31: Will use HISE for residue 60 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS60 31: NE285 31: CYS62 SG98 0.803 31: Making bonds... 31: Number of bonds was 232, now 232 31: Marked 111 virtual sites 31: Added 18 dummy masses 31: Added 31 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 603 pairs 31: Before cleaning: 618 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 618 dihedrals, 48 impropers, 419 angles 31: 597 pairs, 232 bonds and 116 virtual sites 31: Total mass 1662.883 a.m.u. 31: Total charge -0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 117 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (117 atoms, 16 residues) 31: Identified residue LYS50 as a starting terminus. 31: Identified residue PRO65 as a ending terminus. 31: Start terminus LYS-50: NH3+ 31: End terminus PRO-65: PRO-COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 228 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 31: The Oplsaa force field and the tip5p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23 (93 ms) 31: [----------] 24 tests from ForOplsaa/Pdb2gmxTest (2863 ms total) 31: 31: [----------] Global test environment tear-down 31: [==========] 24 tests from 1 test case ran. (2864 ms total) 31: [ PASSED ] 24 tests. 31/54 Test #31: Pdb2gmx1Test ........................ Passed 2.87 sec test 32 Start 32: Pdb2gmx2Test 32: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/pdb2gmx2-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/Pdb2gmx2Test.xml" 32: Test timeout computed to be: 30 32: [==========] Running 32 tests from 2 test cases. 32: [----------] Global test environment set-up. 32: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 25 donors and 23 acceptors were found. 32: There are 41 hydrogen bonds 32: Will use HISE for residue 8 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS3 HIS8 32: SG9 NE251 32: HIS8 NE251 1.055 32: MET12 SD83 0.763 0.990 32: Making bonds... 32: Number of bonds was 172, now 167 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 267 pairs 32: Before cleaning: 305 dihedrals 32: Making cmap torsions... 32: There are 90 dihedrals, 77 impropers, 241 angles 32: 267 pairs, 167 bonds and 0 virtual sites 32: Total mass 1846.116 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 128 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (128 atoms, 16 residues) 32: Identified residue ALA2 as a starting terminus. 32: Identified residue SER17 as a ending terminus. 32: Start terminus ALA-2: NH3+ 32: End terminus SER-17: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 165 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 32: The Gromos43a1 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0 (68 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 30 donors and 22 acceptors were found. 32: There are 36 hydrogen bonds 32: Will use HISE for residue 29 32: Will use HISE for residue 32 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS27 HIS29 32: SG90 NE2111 32: HIS29 NE2111 0.987 32: HIS32 NE2135 1.590 1.155 32: Making bonds... 32: Number of bonds was 216, now 211 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 273 pairs 32: Before cleaning: 429 dihedrals 32: Making cmap torsions... 32: There are 93 dihedrals, 134 impropers, 316 angles 32: 273 pairs, 211 bonds and 0 virtual sites 32: Total mass 2088.361 a.m.u. 32: Total charge 1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 149 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (149 atoms, 16 residues) 32: Identified residue THR18 as a starting terminus. 32: Identified residue PHE33 as a ending terminus. 32: Start terminus THR-18: NH3+ 32: End terminus PHE-33: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 202 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 32: The Gromos43a1 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1 (122 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 22 acceptors were found. 32: There are 26 hydrogen bonds 32: Will use HISE for residue 45 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS45 32: NE295 32: MET46 SD102 1.078 32: Making bonds... 32: Number of bonds was 179, now 174 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 242 pairs 32: Before cleaning: 349 dihedrals 32: Making cmap torsions... 32: There are 81 dihedrals, 102 impropers, 260 angles 32: 242 pairs, 174 bonds and 0 virtual sites 32: Total mass 1861.132 a.m.u. 32: Total charge -1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 132 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (132 atoms, 16 residues) 32: Identified residue ALA34 as a starting terminus. 32: Identified residue ALA49 as a ending terminus. 32: Start terminus ALA-34: NH3+ 32: End terminus ALA-49: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 168 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 32: The Gromos43a1 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2 (87 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 21 acceptors were found. 32: There are 30 hydrogen bonds 32: Will use HISE for residue 60 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS60 32: NE285 32: CYS62 SG98 0.803 32: Making bonds... 32: Number of bonds was 159, now 154 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 232 pairs 32: Before cleaning: 299 dihedrals 32: Making cmap torsions... 32: There are 78 dihedrals, 80 impropers, 227 angles 32: 232 pairs, 154 bonds and 0 virtual sites 32: Total mass 1662.887 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 117 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (117 atoms, 16 residues) 32: Identified residue LYS50 as a starting terminus. 32: Identified residue PRO65 as a ending terminus. 32: Start terminus LYS-50: NH3+ 32: End terminus PRO-65: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 150 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 32: The Gromos43a1 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3 (61 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 25 donors and 23 acceptors were found. 32: There are 41 hydrogen bonds 32: Will use HISE for residue 8 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS3 HIS8 32: SG9 NE251 32: HIS8 NE251 1.055 32: MET12 SD83 0.763 0.990 32: Making bonds... 32: Number of bonds was 172, now 167 32: Marked 37 virtual sites 32: Added 4 dummy masses 32: Added 8 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 267 pairs 32: Before cleaning: 305 dihedrals 32: Making cmap torsions... 32: There are 90 dihedrals, 77 impropers, 241 angles 32: 267 pairs, 167 bonds and 37 virtual sites 32: Total mass 1846.116 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 128 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (128 atoms, 16 residues) 32: Identified residue ALA2 as a starting terminus. 32: Identified residue SER17 as a ending terminus. 32: Start terminus ALA-2: NH3+ 32: End terminus SER-17: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 165 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 32: The Gromos43a1 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4 (64 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 30 donors and 22 acceptors were found. 32: There are 36 hydrogen bonds 32: Will use HISE for residue 29 32: Will use HISE for residue 32 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS27 HIS29 32: SG90 NE2111 32: HIS29 NE2111 0.987 32: HIS32 NE2135 1.590 1.155 32: Making bonds... 32: Number of bonds was 216, now 211 32: Marked 53 virtual sites 32: Added 4 dummy masses 32: Added 10 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 273 pairs 32: Before cleaning: 429 dihedrals 32: Making cmap torsions... 32: There are 93 dihedrals, 134 impropers, 316 angles 32: 273 pairs, 211 bonds and 51 virtual sites 32: Total mass 2088.361 a.m.u. 32: Total charge 1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 149 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (149 atoms, 16 residues) 32: Identified residue THR18 as a starting terminus. 32: Identified residue PHE33 as a ending terminus. 32: Start terminus THR-18: NH3+ 32: End terminus PHE-33: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 202 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 32: The Gromos43a1 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5 (71 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 22 acceptors were found. 32: There are 26 hydrogen bonds 32: Will use HISE for residue 45 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS45 32: NE295 32: MET46 SD102 1.078 32: Making bonds... 32: Number of bonds was 179, now 174 32: Marked 36 virtual sites 32: Added 4 dummy masses 32: Added 8 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 242 pairs 32: Before cleaning: 349 dihedrals 32: Making cmap torsions... 32: There are 81 dihedrals, 102 impropers, 260 angles 32: 242 pairs, 174 bonds and 36 virtual sites 32: Total mass 1861.132 a.m.u. 32: Total charge -1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 132 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (132 atoms, 16 residues) 32: Identified residue ALA34 as a starting terminus. 32: Identified residue ALA49 as a ending terminus. 32: Start terminus ALA-34: NH3+ 32: End terminus ALA-49: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 168 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 32: The Gromos43a1 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6 (45 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 21 acceptors were found. 32: There are 30 hydrogen bonds 32: Will use HISE for residue 60 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS60 32: NE285 32: CYS62 SG98 0.803 32: Making bonds... 32: Number of bonds was 159, now 154 32: Marked 33 virtual sites 32: Added 4 dummy masses 32: Added 10 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 232 pairs 32: Before cleaning: 299 dihedrals 32: Making cmap torsions... 32: There are 78 dihedrals, 80 impropers, 227 angles 32: 232 pairs, 154 bonds and 31 virtual sites 32: Total mass 1662.887 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 117 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (117 atoms, 16 residues) 32: Identified residue LYS50 as a starting terminus. 32: Identified residue PRO65 as a ending terminus. 32: Start terminus LYS-50: NH3+ 32: End terminus PRO-65: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 150 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 32: The Gromos43a1 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7 (73 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 25 donors and 23 acceptors were found. 32: There are 41 hydrogen bonds 32: Will use HISE for residue 8 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS3 HIS8 32: SG9 NE251 32: HIS8 NE251 1.055 32: MET12 SD83 0.763 0.990 32: Making bonds... 32: Number of bonds was 172, now 167 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 267 pairs 32: Before cleaning: 305 dihedrals 32: Making cmap torsions... 32: There are 90 dihedrals, 77 impropers, 241 angles 32: 267 pairs, 167 bonds and 0 virtual sites 32: Total mass 1846.116 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 128 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (128 atoms, 16 residues) 32: Identified residue ALA2 as a starting terminus. 32: Identified residue SER17 as a ending terminus. 32: Start terminus ALA-2: NH3+ 32: End terminus SER-17: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 165 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 32: The Gromos43a1 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8 (87 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 30 donors and 22 acceptors were found. 32: There are 36 hydrogen bonds 32: Will use HISE for residue 29 32: Will use HISE for residue 32 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS27 HIS29 32: SG90 NE2111 32: HIS29 NE2111 0.987 32: HIS32 NE2135 1.590 1.155 32: Making bonds... 32: Number of bonds was 216, now 211 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 273 pairs 32: Before cleaning: 429 dihedrals 32: Making cmap torsions... 32: There are 93 dihedrals, 134 impropers, 316 angles 32: 273 pairs, 211 bonds and 0 virtual sites 32: Total mass 2088.361 a.m.u. 32: Total charge 1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 149 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (149 atoms, 16 residues) 32: Identified residue THR18 as a starting terminus. 32: Identified residue PHE33 as a ending terminus. 32: Start terminus THR-18: NH3+ 32: End terminus PHE-33: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 202 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 32: The Gromos43a1 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9 (50 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 22 acceptors were found. 32: There are 26 hydrogen bonds 32: Will use HISE for residue 45 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS45 32: NE295 32: MET46 SD102 1.078 32: Making bonds... 32: Number of bonds was 179, now 174 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 242 pairs 32: Before cleaning: 349 dihedrals 32: Making cmap torsions... 32: There are 81 dihedrals, 102 impropers, 260 angles 32: 242 pairs, 174 bonds and 0 virtual sites 32: Total mass 1861.132 a.m.u. 32: Total charge -1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 132 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (132 atoms, 16 residues) 32: Identified residue ALA34 as a starting terminus. 32: Identified residue ALA49 as a ending terminus. 32: Start terminus ALA-34: NH3+ 32: End terminus ALA-49: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 168 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 32: The Gromos43a1 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10 (58 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 21 acceptors were found. 32: There are 30 hydrogen bonds 32: Will use HISE for residue 60 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS60 32: NE285 32: CYS62 SG98 0.803 32: Making bonds... 32: Number of bonds was 159, now 154 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 232 pairs 32: Before cleaning: 299 dihedrals 32: Making cmap torsions... 32: There are 78 dihedrals, 80 impropers, 227 angles 32: 232 pairs, 154 bonds and 0 virtual sites 32: Total mass 1662.887 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 117 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (117 atoms, 16 residues) 32: Identified residue LYS50 as a starting terminus. 32: Identified residue PRO65 as a ending terminus. 32: Start terminus LYS-50: NH3+ 32: End terminus PRO-65: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 150 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 32: The Gromos43a1 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11 (49 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 25 donors and 23 acceptors were found. 32: There are 41 hydrogen bonds 32: Will use HISE for residue 8 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS3 HIS8 32: SG9 NE251 32: HIS8 NE251 1.055 32: MET12 SD83 0.763 0.990 32: Making bonds... 32: Number of bonds was 172, now 167 32: Marked 37 virtual sites 32: Added 4 dummy masses 32: Added 8 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 267 pairs 32: Before cleaning: 305 dihedrals 32: Making cmap torsions... 32: There are 90 dihedrals, 77 impropers, 241 angles 32: 267 pairs, 167 bonds and 37 virtual sites 32: Total mass 1846.116 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 128 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (128 atoms, 16 residues) 32: Identified residue ALA2 as a starting terminus. 32: Identified residue SER17 as a ending terminus. 32: Start terminus ALA-2: NH3+ 32: End terminus SER-17: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 165 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 32: The Gromos43a1 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12 (64 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 30 donors and 22 acceptors were found. 32: There are 36 hydrogen bonds 32: Will use HISE for residue 29 32: Will use HISE for residue 32 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS27 HIS29 32: SG90 NE2111 32: HIS29 NE2111 0.987 32: HIS32 NE2135 1.590 1.155 32: Making bonds... 32: Number of bonds was 216, now 211 32: Marked 53 virtual sites 32: Added 4 dummy masses 32: Added 10 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 273 pairs 32: Before cleaning: 429 dihedrals 32: Making cmap torsions... 32: There are 93 dihedrals, 134 impropers, 316 angles 32: 273 pairs, 211 bonds and 51 virtual sites 32: Total mass 2088.361 a.m.u. 32: Total charge 1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 149 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (149 atoms, 16 residues) 32: Identified residue THR18 as a starting terminus. 32: Identified residue PHE33 as a ending terminus. 32: Start terminus THR-18: NH3+ 32: End terminus PHE-33: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 202 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 32: The Gromos43a1 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13 (81 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 22 acceptors were found. 32: There are 26 hydrogen bonds 32: Will use HISE for residue 45 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS45 32: NE295 32: MET46 SD102 1.078 32: Making bonds... 32: Number of bonds was 179, now 174 32: Marked 36 virtual sites 32: Added 4 dummy masses 32: Added 8 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 242 pairs 32: Before cleaning: 349 dihedrals 32: Making cmap torsions... 32: There are 81 dihedrals, 102 impropers, 260 angles 32: 242 pairs, 174 bonds and 36 virtual sites 32: Total mass 1861.132 a.m.u. 32: Total charge -1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 132 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (132 atoms, 16 residues) 32: Identified residue ALA34 as a starting terminus. 32: Identified residue ALA49 as a ending terminus. 32: Start terminus ALA-34: NH3+ 32: End terminus ALA-49: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 168 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 32: The Gromos43a1 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14 (96 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 21 acceptors were found. 32: There are 30 hydrogen bonds 32: Will use HISE for residue 60 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS60 32: NE285 32: CYS62 SG98 0.803 32: Making bonds... 32: Number of bonds was 159, now 154 32: Marked 33 virtual sites 32: Added 4 dummy masses 32: Added 10 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 232 pairs 32: Before cleaning: 299 dihedrals 32: Making cmap torsions... 32: There are 78 dihedrals, 80 impropers, 227 angles 32: 232 pairs, 154 bonds and 31 virtual sites 32: Total mass 1662.887 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 117 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (117 atoms, 16 residues) 32: Identified residue LYS50 as a starting terminus. 32: Identified residue PRO65 as a ending terminus. 32: Start terminus LYS-50: NH3+ 32: End terminus PRO-65: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 150 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 32: The Gromos43a1 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15 (98 ms) 32: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest (1177 ms total) 32: 32: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 25 donors and 23 acceptors were found. 32: There are 41 hydrogen bonds 32: Will use HISE for residue 8 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS3 HIS8 32: SG9 NE251 32: HIS8 NE251 1.055 32: MET12 SD83 0.763 0.990 32: Making bonds... 32: Number of bonds was 174, now 169 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 267 pairs 32: Before cleaning: 312 dihedrals 32: Making cmap torsions... 32: There are 90 dihedrals, 79 impropers, 245 angles 32: 267 pairs, 169 bonds and 0 virtual sites 32: Total mass 1846.116 a.m.u. 32: Total charge -0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 128 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (128 atoms, 16 residues) 32: Identified residue ALA2 as a starting terminus. 32: Identified residue SER17 as a ending terminus. 32: Start terminus ALA-2: NH3+ 32: End terminus SER-17: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 167 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 32: The Gromos53a6 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0 (55 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 30 donors and 22 acceptors were found. 32: There are 36 hydrogen bonds 32: Will use HISE for residue 29 32: Will use HISE for residue 32 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS27 HIS29 32: SG90 NE2111 32: HIS29 NE2111 0.987 32: HIS32 NE2135 1.590 1.155 32: Making bonds... 32: Number of bonds was 220, now 215 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 273 pairs 32: Before cleaning: 443 dihedrals 32: Making cmap torsions... 32: There are 93 dihedrals, 138 impropers, 324 angles 32: 273 pairs, 215 bonds and 0 virtual sites 32: Total mass 2088.361 a.m.u. 32: Total charge 1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 149 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (149 atoms, 16 residues) 32: Identified residue THR18 as a starting terminus. 32: Identified residue PHE33 as a ending terminus. 32: Start terminus THR-18: NH3+ 32: End terminus PHE-33: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 206 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 32: The Gromos53a6 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1 (94 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 22 acceptors were found. 32: There are 26 hydrogen bonds 32: Will use HISE for residue 45 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS45 32: NE295 32: MET46 SD102 1.078 32: Making bonds... 32: Number of bonds was 181, now 176 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 242 pairs 32: Before cleaning: 356 dihedrals 32: Making cmap torsions... 32: There are 81 dihedrals, 104 impropers, 264 angles 32: 242 pairs, 176 bonds and 0 virtual sites 32: Total mass 1861.132 a.m.u. 32: Total charge -1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 132 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (132 atoms, 16 residues) 32: Identified residue ALA34 as a starting terminus. 32: Identified residue ALA49 as a ending terminus. 32: Start terminus ALA-34: NH3+ 32: End terminus ALA-49: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 170 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 32: The Gromos53a6 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2 (93 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 21 acceptors were found. 32: There are 30 hydrogen bonds 32: Will use HISE for residue 60 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS60 32: NE285 32: CYS62 SG98 0.803 32: Making bonds... 32: Number of bonds was 161, now 156 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 232 pairs 32: Before cleaning: 306 dihedrals 32: Making cmap torsions... 32: There are 78 dihedrals, 82 impropers, 231 angles 32: 232 pairs, 156 bonds and 0 virtual sites 32: Total mass 1662.887 a.m.u. 32: Total charge -0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 117 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (117 atoms, 16 residues) 32: Identified residue LYS50 as a starting terminus. 32: Identified residue PRO65 as a ending terminus. 32: Start terminus LYS-50: NH3+ 32: End terminus PRO-65: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 152 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 32: The Gromos53a6 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3 (86 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 25 donors and 23 acceptors were found. 32: There are 41 hydrogen bonds 32: Will use HISE for residue 8 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS3 HIS8 32: SG9 NE251 32: HIS8 NE251 1.055 32: MET12 SD83 0.763 0.990 32: Making bonds... 32: Number of bonds was 174, now 169 32: Marked 39 virtual sites 32: Added 4 dummy masses 32: Added 8 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 267 pairs 32: Before cleaning: 312 dihedrals 32: Making cmap torsions... 32: There are 90 dihedrals, 79 impropers, 245 angles 32: 267 pairs, 169 bonds and 39 virtual sites 32: Total mass 1846.116 a.m.u. 32: Total charge -0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 128 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (128 atoms, 16 residues) 32: Identified residue ALA2 as a starting terminus. 32: Identified residue SER17 as a ending terminus. 32: Start terminus ALA-2: NH3+ 32: End terminus SER-17: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 167 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 32: The Gromos53a6 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4 (82 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 30 donors and 22 acceptors were found. 32: There are 36 hydrogen bonds 32: Will use HISE for residue 29 32: Will use HISE for residue 32 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS27 HIS29 32: SG90 NE2111 32: HIS29 NE2111 0.987 32: HIS32 NE2135 1.590 1.155 32: Making bonds... 32: Number of bonds was 220, now 215 32: Marked 57 virtual sites 32: Added 4 dummy masses 32: Added 10 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 273 pairs 32: Before cleaning: 443 dihedrals 32: Making cmap torsions... 32: There are 93 dihedrals, 138 impropers, 324 angles 32: 273 pairs, 215 bonds and 55 virtual sites 32: Total mass 2088.361 a.m.u. 32: Total charge 1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 149 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (149 atoms, 16 residues) 32: Identified residue THR18 as a starting terminus. 32: Identified residue PHE33 as a ending terminus. 32: Start terminus THR-18: NH3+ 32: End terminus PHE-33: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 206 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 32: The Gromos53a6 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5 (124 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 22 acceptors were found. 32: There are 26 hydrogen bonds 32: Will use HISE for residue 45 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS45 32: NE295 32: MET46 SD102 1.078 32: Making bonds... 32: Number of bonds was 181, now 176 32: Marked 38 virtual sites 32: Added 4 dummy masses 32: Added 8 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 242 pairs 32: Before cleaning: 356 dihedrals 32: Making cmap torsions... 32: There are 81 dihedrals, 104 impropers, 264 angles 32: 242 pairs, 176 bonds and 38 virtual sites 32: Total mass 1861.132 a.m.u. 32: Total charge -1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 132 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (132 atoms, 16 residues) 32: Identified residue ALA34 as a starting terminus. 32: Identified residue ALA49 as a ending terminus. 32: Start terminus ALA-34: NH3+ 32: End terminus ALA-49: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 170 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 32: The Gromos53a6 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6 (97 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 21 acceptors were found. 32: There are 30 hydrogen bonds 32: Will use HISE for residue 60 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS60 32: NE285 32: CYS62 SG98 0.803 32: Making bonds... 32: Number of bonds was 161, now 156 32: Marked 35 virtual sites 32: Added 4 dummy masses 32: Added 10 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 232 pairs 32: Before cleaning: 306 dihedrals 32: Making cmap torsions... 32: There are 78 dihedrals, 82 impropers, 231 angles 32: 232 pairs, 156 bonds and 33 virtual sites 32: Total mass 1662.887 a.m.u. 32: Total charge -0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 117 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (117 atoms, 16 residues) 32: Identified residue LYS50 as a starting terminus. 32: Identified residue PRO65 as a ending terminus. 32: Start terminus LYS-50: NH3+ 32: End terminus PRO-65: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 152 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 32: The Gromos53a6 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7 (94 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 25 donors and 23 acceptors were found. 32: There are 41 hydrogen bonds 32: Will use HISE for residue 8 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS3 HIS8 32: SG9 NE251 32: HIS8 NE251 1.055 32: MET12 SD83 0.763 0.990 32: Making bonds... 32: Number of bonds was 174, now 169 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 267 pairs 32: Before cleaning: 312 dihedrals 32: Making cmap torsions... 32: There are 90 dihedrals, 79 impropers, 245 angles 32: 267 pairs, 169 bonds and 0 virtual sites 32: Total mass 1846.116 a.m.u. 32: Total charge -0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 128 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (128 atoms, 16 residues) 32: Identified residue ALA2 as a starting terminus. 32: Identified residue SER17 as a ending terminus. 32: Start terminus ALA-2: NH3+ 32: End terminus SER-17: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 167 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 32: The Gromos53a6 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8 (92 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 30 donors and 22 acceptors were found. 32: There are 36 hydrogen bonds 32: Will use HISE for residue 29 32: Will use HISE for residue 32 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS27 HIS29 32: SG90 NE2111 32: HIS29 NE2111 0.987 32: HIS32 NE2135 1.590 1.155 32: Making bonds... 32: Number of bonds was 220, now 215 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 273 pairs 32: Before cleaning: 443 dihedrals 32: Making cmap torsions... 32: There are 93 dihedrals, 138 impropers, 324 angles 32: 273 pairs, 215 bonds and 0 virtual sites 32: Total mass 2088.361 a.m.u. 32: Total charge 1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 149 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (149 atoms, 16 residues) 32: Identified residue THR18 as a starting terminus. 32: Identified residue PHE33 as a ending terminus. 32: Start terminus THR-18: NH3+ 32: End terminus PHE-33: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 206 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 32: The Gromos53a6 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9 (112 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 22 acceptors were found. 32: There are 26 hydrogen bonds 32: Will use HISE for residue 45 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS45 32: NE295 32: MET46 SD102 1.078 32: Making bonds... 32: Number of bonds was 181, now 176 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 242 pairs 32: Before cleaning: 356 dihedrals 32: Making cmap torsions... 32: There are 81 dihedrals, 104 impropers, 264 angles 32: 242 pairs, 176 bonds and 0 virtual sites 32: Total mass 1861.132 a.m.u. 32: Total charge -1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 132 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (132 atoms, 16 residues) 32: Identified residue ALA34 as a starting terminus. 32: Identified residue ALA49 as a ending terminus. 32: Start terminus ALA-34: NH3+ 32: End terminus ALA-49: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 170 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 32: The Gromos53a6 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10 (46 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 21 acceptors were found. 32: There are 30 hydrogen bonds 32: Will use HISE for residue 60 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS60 32: NE285 32: CYS62 SG98 0.803 32: Making bonds... 32: Number of bonds was 161, now 156 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 232 pairs 32: Before cleaning: 306 dihedrals 32: Making cmap torsions... 32: There are 78 dihedrals, 82 impropers, 231 angles 32: 232 pairs, 156 bonds and 0 virtual sites 32: Total mass 1662.887 a.m.u. 32: Total charge -0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 117 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (117 atoms, 16 residues) 32: Identified residue LYS50 as a starting terminus. 32: Identified residue PRO65 as a ending terminus. 32: Start terminus LYS-50: NH3+ 32: End terminus PRO-65: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 152 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 32: The Gromos53a6 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11 (55 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 25 donors and 23 acceptors were found. 32: There are 41 hydrogen bonds 32: Will use HISE for residue 8 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS3 HIS8 32: SG9 NE251 32: HIS8 NE251 1.055 32: MET12 SD83 0.763 0.990 32: Making bonds... 32: Number of bonds was 174, now 169 32: Marked 39 virtual sites 32: Added 4 dummy masses 32: Added 8 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 267 pairs 32: Before cleaning: 312 dihedrals 32: Making cmap torsions... 32: There are 90 dihedrals, 79 impropers, 245 angles 32: 267 pairs, 169 bonds and 39 virtual sites 32: Total mass 1846.116 a.m.u. 32: Total charge -0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 128 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (128 atoms, 16 residues) 32: Identified residue ALA2 as a starting terminus. 32: Identified residue SER17 as a ending terminus. 32: Start terminus ALA-2: NH3+ 32: End terminus SER-17: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 167 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 32: The Gromos53a6 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12 (80 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 30 donors and 22 acceptors were found. 32: There are 36 hydrogen bonds 32: Will use HISE for residue 29 32: Will use HISE for residue 32 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS27 HIS29 32: SG90 NE2111 32: HIS29 NE2111 0.987 32: HIS32 NE2135 1.590 1.155 32: Making bonds... 32: Number of bonds was 220, now 215 32: Marked 57 virtual sites 32: Added 4 dummy masses 32: Added 10 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 273 pairs 32: Before cleaning: 443 dihedrals 32: Making cmap torsions... 32: There are 93 dihedrals, 138 impropers, 324 angles 32: 273 pairs, 215 bonds and 55 virtual sites 32: Total mass 2088.361 a.m.u. 32: Total charge 1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 149 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (149 atoms, 16 residues) 32: Identified residue THR18 as a starting terminus. 32: Identified residue PHE33 as a ending terminus. 32: Start terminus THR-18: NH3+ 32: End terminus PHE-33: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 206 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 32: The Gromos53a6 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13 (76 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 22 acceptors were found. 32: There are 26 hydrogen bonds 32: Will use HISE for residue 45 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS45 32: NE295 32: MET46 SD102 1.078 32: Making bonds... 32: Number of bonds was 181, now 176 32: Marked 38 virtual sites 32: Added 4 dummy masses 32: Added 8 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 242 pairs 32: Before cleaning: 356 dihedrals 32: Making cmap torsions... 32: There are 81 dihedrals, 104 impropers, 264 angles 32: 242 pairs, 176 bonds and 38 virtual sites 32: Total mass 1861.132 a.m.u. 32: Total charge -1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 132 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (132 atoms, 16 residues) 32: Identified residue ALA34 as a starting terminus. 32: Identified residue ALA49 as a ending terminus. 32: Start terminus ALA-34: NH3+ 32: End terminus ALA-49: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 170 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 32: The Gromos53a6 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14 (54 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 21 acceptors were found. 32: There are 30 hydrogen bonds 32: Will use HISE for residue 60 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS60 32: NE285 32: CYS62 SG98 0.803 32: Making bonds... 32: Number of bonds was 161, now 156 32: Marked 35 virtual sites 32: Added 4 dummy masses 32: Added 10 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 232 pairs 32: Before cleaning: 306 dihedrals 32: Making cmap torsions... 32: There are 78 dihedrals, 82 impropers, 231 angles 32: 232 pairs, 156 bonds and 33 virtual sites 32: Total mass 1662.887 a.m.u. 32: Total charge -0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 117 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (117 atoms, 16 residues) 32: Identified residue LYS50 as a starting terminus. 32: Identified residue PRO65 as a ending terminus. 32: Start terminus LYS-50: NH3+ 32: End terminus PRO-65: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 152 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 32: The Gromos53a6 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15 (72 ms) 32: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest (1314 ms total) 32: 32: [----------] Global test environment tear-down 32: [==========] 32 tests from 2 test cases ran. (2491 ms total) 32: [ PASSED ] 32 tests. 32/54 Test #32: Pdb2gmx2Test ........................ Passed 2.50 sec test 33 Start 33: Pdb2gmx3Test 33: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/pdb2gmx3-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/Pdb2gmx3Test.xml" 33: Test timeout computed to be: 30 33: [==========] Running 28 tests from 4 test cases. 33: [----------] Global test environment set-up. 33: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest 33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 25 donors and 23 acceptors were found. 33: There are 41 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 HIS8 33: SG9 NE251 33: HIS8 NE251 1.055 33: MET12 SD83 0.763 0.990 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.arn 33: Making bonds... 33: Number of bonds was 255, now 254 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 653 pairs 33: Before cleaning: 691 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 691 dihedrals, 51 impropers, 457 angles 33: 650 pairs, 254 bonds and 0 virtual sites 33: Total mass 1846.132 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 33: 33: going to rename amber99sb-ildn.ff/aminoacids.r2b 33: going to rename amber99sb-ildn.ff/dna.r2b 33: going to rename amber99sb-ildn.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 128 33: 33: Reading residue database... (Amber99sb-ildn) 33: Processing chain 1 (128 atoms, 16 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 252 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 33: The Amber99sb-ildn force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0 (119 ms) 33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 30 donors and 22 acceptors were found. 33: There are 36 hydrogen bonds 33: Will use HISE for residue 29 33: Will use HISE for residue 32 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS27 HIS29 33: SG90 NE2111 33: HIS29 NE2111 0.987 33: HIS32 NE2135 1.590 1.155 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.arn 33: Making bonds... 33: Number of bonds was 291, now 290 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 748 pairs 33: Before cleaning: 788 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 788 dihedrals, 72 impropers, 516 angles 33: 736 pairs, 290 bonds and 0 virtual sites 33: Total mass 2088.366 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 33: 33: going to rename amber99sb-ildn.ff/aminoacids.r2b 33: going to rename amber99sb-ildn.ff/dna.r2b 33: going to rename amber99sb-ildn.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 149 33: 33: Reading residue database... (Amber99sb-ildn) 33: Processing chain 1 (149 atoms, 16 residues) 33: Identified residue THR18 as a starting terminus. 33: Identified residue PHE33 as a ending terminus. 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 281 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 33: The Amber99sb-ildn force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1 (89 ms) 33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 22 donors and 22 acceptors were found. 33: There are 26 hydrogen bonds 33: Will use HISE for residue 45 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: HIS45 33: NE295 33: MET46 SD102 1.078 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.arn 33: Making bonds... 33: Number of bonds was 262, now 261 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 676 pairs 33: Before cleaning: 727 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 727 dihedrals, 56 impropers, 472 angles 33: 667 pairs, 261 bonds and 0 virtual sites 33: Total mass 1861.124 a.m.u. 33: Total charge -1.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 33: 33: going to rename amber99sb-ildn.ff/aminoacids.r2b 33: going to rename amber99sb-ildn.ff/dna.r2b 33: going to rename amber99sb-ildn.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 132 33: 33: Reading residue database... (Amber99sb-ildn) 33: Processing chain 1 (132 atoms, 16 residues) 33: Identified residue ALA34 as a starting terminus. 33: Identified residue ALA49 as a ending terminus. 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 255 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 33: The Amber99sb-ildn force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2 (92 ms) 33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 22 donors and 21 acceptors were found. 33: There are 30 hydrogen bonds 33: Will use HISE for residue 60 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: HIS60 33: NE285 33: CYS62 SG98 0.803 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.arn 33: Making bonds... 33: Number of bonds was 233, now 232 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 603 pairs 33: Before cleaning: 634 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 634 dihedrals, 48 impropers, 419 angles 33: 597 pairs, 232 bonds and 0 virtual sites 33: Total mass 1662.888 a.m.u. 33: Total charge -0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 33: 33: going to rename amber99sb-ildn.ff/aminoacids.r2b 33: going to rename amber99sb-ildn.ff/dna.r2b 33: going to rename amber99sb-ildn.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 117 33: 33: Reading residue database... (Amber99sb-ildn) 33: Processing chain 1 (117 atoms, 16 residues) 33: Identified residue LYS50 as a starting terminus. 33: Identified residue PRO65 as a ending terminus. 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 228 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 33: The Amber99sb-ildn force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3 (82 ms) 33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 25 donors and 23 acceptors were found. 33: There are 41 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 HIS8 33: SG9 NE251 33: HIS8 NE251 1.055 33: MET12 SD83 0.763 0.990 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.arn 33: Making bonds... 33: Number of bonds was 255, now 254 33: Marked 124 virtual sites 33: Added 16 dummy masses 33: Added 26 new constraints 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 653 pairs 33: Before cleaning: 691 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 691 dihedrals, 51 impropers, 457 angles 33: 650 pairs, 254 bonds and 130 virtual sites 33: Total mass 1846.132 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 33: 33: going to rename amber99sb-ildn.ff/aminoacids.r2b 33: going to rename amber99sb-ildn.ff/dna.r2b 33: going to rename amber99sb-ildn.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 128 33: 33: Reading residue database... (Amber99sb-ildn) 33: Processing chain 1 (128 atoms, 16 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 252 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 33: The Amber99sb-ildn force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4 (104 ms) 33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 30 donors and 22 acceptors were found. 33: There are 36 hydrogen bonds 33: Will use HISE for residue 29 33: Will use HISE for residue 32 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS27 HIS29 33: SG90 NE2111 33: HIS29 NE2111 0.987 33: HIS32 NE2135 1.590 1.155 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.arn 33: Making bonds... 33: Number of bonds was 291, now 290 33: Marked 132 virtual sites 33: Added 10 dummy masses 33: Added 19 new constraints 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 748 pairs 33: Before cleaning: 788 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 788 dihedrals, 72 impropers, 516 angles 33: 736 pairs, 290 bonds and 133 virtual sites 33: Total mass 2088.366 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 33: 33: going to rename amber99sb-ildn.ff/aminoacids.r2b 33: going to rename amber99sb-ildn.ff/dna.r2b 33: going to rename amber99sb-ildn.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 149 33: 33: Reading residue database... (Amber99sb-ildn) 33: Processing chain 1 (149 atoms, 16 residues) 33: Identified residue THR18 as a starting terminus. 33: Identified residue PHE33 as a ending terminus. 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 281 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 33: The Amber99sb-ildn force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5 (93 ms) 33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 22 donors and 22 acceptors were found. 33: There are 26 hydrogen bonds 33: Will use HISE for residue 45 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: HIS45 33: NE295 33: MET46 SD102 1.078 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.arn 33: Making bonds... 33: Number of bonds was 262, now 261 33: Marked 123 virtual sites 33: Added 22 dummy masses 33: Added 35 new constraints 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 676 pairs 33: Before cleaning: 727 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 727 dihedrals, 56 impropers, 472 angles 33: 667 pairs, 261 bonds and 132 virtual sites 33: Total mass 1861.124 a.m.u. 33: Total charge -1.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 33: 33: going to rename amber99sb-ildn.ff/aminoacids.r2b 33: going to rename amber99sb-ildn.ff/dna.r2b 33: going to rename amber99sb-ildn.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 132 33: 33: Reading residue database... (Amber99sb-ildn) 33: Processing chain 1 (132 atoms, 16 residues) 33: Identified residue ALA34 as a starting terminus. 33: Identified residue ALA49 as a ending terminus. 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 255 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 33: The Amber99sb-ildn force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6 (94 ms) 33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 22 donors and 21 acceptors were found. 33: There are 30 hydrogen bonds 33: Will use HISE for residue 60 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: HIS60 33: NE285 33: CYS62 SG98 0.803 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.arn 33: Making bonds... 33: Number of bonds was 233, now 232 33: Marked 111 virtual sites 33: Added 18 dummy masses 33: Added 31 new constraints 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 603 pairs 33: Before cleaning: 634 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 634 dihedrals, 48 impropers, 419 angles 33: 597 pairs, 232 bonds and 116 virtual sites 33: Total mass 1662.888 a.m.u. 33: Total charge -0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 33: 33: going to rename amber99sb-ildn.ff/aminoacids.r2b 33: going to rename amber99sb-ildn.ff/dna.r2b 33: going to rename amber99sb-ildn.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 117 33: 33: Reading residue database... (Amber99sb-ildn) 33: Processing chain 1 (117 atoms, 16 residues) 33: Identified residue LYS50 as a starting terminus. 33: Identified residue PRO65 as a ending terminus. 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 228 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 33: The Amber99sb-ildn force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7 (59 ms) 33: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest (732 ms total) 33: 33: [----------] 8 tests from ForCharmm27/Pdb2gmxTest 33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 25 donors and 23 acceptors were found. 33: There are 41 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 HIS8 33: SG9 NE251 33: HIS8 NE251 1.055 33: MET12 SD83 0.763 0.990 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 254, now 254 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 653 pairs 33: Before cleaning: 663 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 14 cmap torsion pairs 33: There are 663 dihedrals, 48 impropers, 457 angles 33: 650 pairs, 254 bonds and 0 virtual sites 33: Total mass 1846.115 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 128 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 (128 atoms, 16 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 252 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0 (90 ms) 33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 30 donors and 22 acceptors were found. 33: There are 36 hydrogen bonds 33: Will use HISE for residue 29 33: Will use HISE for residue 32 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS27 HIS29 33: SG90 NE2111 33: HIS29 NE2111 0.987 33: HIS32 NE2135 1.590 1.155 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 290, now 290 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 748 pairs 33: Before cleaning: 778 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 14 cmap torsion pairs 33: There are 778 dihedrals, 49 impropers, 516 angles 33: 736 pairs, 290 bonds and 0 virtual sites 33: Total mass 2088.361 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 149 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 (149 atoms, 16 residues) 33: Identified residue THR18 as a starting terminus. 33: Identified residue PHE33 as a ending terminus. 33: Start terminus THR-18: NH3+ 33: End terminus PHE-33: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 281 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1 (92 ms) 33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 22 donors and 22 acceptors were found. 33: There are 26 hydrogen bonds 33: Will use HISE for residue 45 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: HIS45 33: NE295 33: MET46 SD102 1.078 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 261, now 261 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 676 pairs 33: Before cleaning: 696 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 14 cmap torsion pairs 33: There are 696 dihedrals, 39 impropers, 472 angles 33: 667 pairs, 261 bonds and 0 virtual sites 33: Total mass 1861.130 a.m.u. 33: Total charge -1.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 132 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 (132 atoms, 16 residues) 33: Identified residue ALA34 as a starting terminus. 33: Identified residue ALA49 as a ending terminus. 33: Start terminus ALA-34: NH3+ 33: End terminus ALA-49: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 255 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2 (98 ms) 33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 22 donors and 21 acceptors were found. 33: There are 30 hydrogen bonds 33: Will use HISE for residue 60 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: HIS60 33: NE285 33: CYS62 SG98 0.803 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 232, now 232 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 603 pairs 33: Before cleaning: 618 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 14 cmap torsion pairs 33: There are 618 dihedrals, 38 impropers, 419 angles 33: 597 pairs, 232 bonds and 0 virtual sites 33: Total mass 1662.885 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 117 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 (117 atoms, 16 residues) 33: Identified residue LYS50 as a starting terminus. 33: Identified residue PRO65 as a ending terminus. 33: Start terminus LYS-50: NH3+ 33: End terminus PRO-65: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 228 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3 (291 ms) 33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 25 donors and 23 acceptors were found. 33: There are 41 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 HIS8 33: SG9 NE251 33: HIS8 NE251 1.055 33: MET12 SD83 0.763 0.990 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 254, now 254 33: Marked 124 virtual sites 33: Added 16 dummy masses 33: Added 26 new constraints 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 653 pairs 33: Before cleaning: 663 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 14 cmap torsion pairs 33: There are 663 dihedrals, 48 impropers, 457 angles 33: 650 pairs, 254 bonds and 130 virtual sites 33: Total mass 1846.115 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 128 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 (128 atoms, 16 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 252 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4 (303 ms) 33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 30 donors and 22 acceptors were found. 33: There are 36 hydrogen bonds 33: Will use HISE for residue 29 33: Will use HISE for residue 32 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS27 HIS29 33: SG90 NE2111 33: HIS29 NE2111 0.987 33: HIS32 NE2135 1.590 1.155 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 290, now 290 33: Marked 132 virtual sites 33: Added 10 dummy masses 33: Added 19 new constraints 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 748 pairs 33: Before cleaning: 778 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 14 cmap torsion pairs 33: There are 778 dihedrals, 49 impropers, 516 angles 33: 736 pairs, 290 bonds and 133 virtual sites 33: Total mass 2088.361 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 149 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 (149 atoms, 16 residues) 33: Identified residue THR18 as a starting terminus. 33: Identified residue PHE33 as a ending terminus. 33: Start terminus THR-18: NH3+ 33: End terminus PHE-33: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 281 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5 (114 ms) 33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 22 donors and 22 acceptors were found. 33: There are 26 hydrogen bonds 33: Will use HISE for residue 45 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: HIS45 33: NE295 33: MET46 SD102 1.078 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 261, now 261 33: Marked 123 virtual sites 33: Added 22 dummy masses 33: Added 35 new constraints 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 676 pairs 33: Before cleaning: 696 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 14 cmap torsion pairs 33: There are 696 dihedrals, 39 impropers, 472 angles 33: 667 pairs, 261 bonds and 132 virtual sites 33: Total mass 1861.130 a.m.u. 33: Total charge -1.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 132 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 (132 atoms, 16 residues) 33: Identified residue ALA34 as a starting terminus. 33: Identified residue ALA49 as a ending terminus. 33: Start terminus ALA-34: NH3+ 33: End terminus ALA-49: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 255 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6 (146 ms) 33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 22 donors and 21 acceptors were found. 33: There are 30 hydrogen bonds 33: Will use HISE for residue 60 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: HIS60 33: NE285 33: CYS62 SG98 0.803 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 232, now 232 33: Marked 111 virtual sites 33: Added 18 dummy masses 33: Added 31 new constraints 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 603 pairs 33: Before cleaning: 618 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 14 cmap torsion pairs 33: There are 618 dihedrals, 38 impropers, 419 angles 33: 597 pairs, 232 bonds and 116 virtual sites 33: Total mass 1662.885 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 117 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 (117 atoms, 16 residues) 33: Identified residue LYS50 as a starting terminus. 33: Identified residue PRO65 as a ending terminus. 33: Start terminus LYS-50: NH3+ 33: End terminus PRO-65: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 228 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7 (133 ms) 33: [----------] 8 tests from ForCharmm27/Pdb2gmxTest (1268 ms total) 33: 33: [----------] 8 tests from ChainSep/Pdb2gmxTest 33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 25 donors and 23 acceptors were found. 33: There are 41 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 HIS8 33: SG9 NE251 33: HIS8 NE251 1.055 33: MET12 SD83 0.763 0.990 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 258, now 258 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 651 pairs 33: Before cleaning: 661 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 10 cmap torsion pairs 33: There are 661 dihedrals, 46 impropers, 463 angles 33: 648 pairs, 258 bonds and 0 virtual sites 33: Total mass 1882.146 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on changing chain id only (ignoring TER records). 33: 33: Merged chains into joint molecule definitions at 2 places. 33: 33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 33: 33: chain #res #atoms 33: 1 'A' 16 127 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (127 atoms, 16 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue GLU5 as a ending terminus. 33: Identified residue PHE6 as a starting terminus. 33: Identified residue MET12 as a ending terminus. 33: Identified residue ASN13 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus GLU-5: COO- 33: Start terminus PHE-6: NH3+ 33: End terminus MET-12: COO- 33: Start terminus ASN-13: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 258 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0 (176 ms) 33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 50, now 50 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 123 pairs 33: Before cleaning: 123 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 2 cmap torsion pairs 33: There are 123 dihedrals, 9 impropers, 88 angles 33: 123 pairs, 50 bonds and 0 virtual sites 33: Total mass 434.421 a.m.u. 33: Total charge -2.000 e 33: Writing topology 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 10 donors and 7 acceptors were found. 33: There are 7 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: HIS8 33: NE223 33: MET12 SD55 0.990 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 125, now 125 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 317 pairs 33: Before cleaning: 322 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 5 cmap torsion pairs 33: There are 322 dihedrals, 19 impropers, 227 angles 33: 314 pairs, 125 bonds and 0 virtual sites 33: Total mass 846.083 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 83, now 83 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 211 pairs 33: Before cleaning: 216 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 3 cmap torsion pairs 33: There are 216 dihedrals, 18 impropers, 148 angles 33: 211 pairs, 83 bonds and 0 virtual sites 33: Total mass 601.643 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: Now there are 258 atoms and 16 residues 33: Total mass in system 1882.146 a.m.u. 33: Total charge in system 0.000 e 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on changing chain id only (ignoring TER records). 33: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 33: 33: chain #res #atoms 33: 1 'A' 4 28 33: 2 'B' 7 58 33: 3 'C' 5 41 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (28 atoms, 4 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue GLU5 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus GLU-5: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 4 residues with 51 atoms 33: Chain time... 33: Processing chain 2 'B' (58 atoms, 7 residues) 33: Identified residue PHE6 as a starting terminus. 33: Identified residue MET12 as a ending terminus. 33: Start terminus PHE-6: NH3+ 33: End terminus MET-12: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 7 residues with 124 atoms 33: Chain time... 33: Processing chain 3 'C' (41 atoms, 5 residues) 33: Identified residue ASN13 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ASN-13: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 5 residues with 83 atoms 33: Chain time... 33: Including chain 1 in system: 51 atoms 4 residues 33: Including chain 2 in system: 124 atoms 7 residues 33: Including chain 3 in system: 83 atoms 5 residues 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1 (87 ms) 33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 25 donors and 23 acceptors were found. 33: There are 41 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 HIS8 33: SG9 NE251 33: HIS8 NE251 1.055 33: MET12 SD83 0.763 0.990 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 258, now 258 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 651 pairs 33: Before cleaning: 661 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 10 cmap torsion pairs 33: There are 661 dihedrals, 46 impropers, 463 angles 33: 648 pairs, 258 bonds and 0 virtual sites 33: Total mass 1882.146 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records only (ignoring chain id). 33: 33: Merged chains into joint molecule definitions at 2 places. 33: 33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 33: 33: chain #res #atoms 33: 1 'A' 16 127 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (127 atoms, 16 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue ILE9 as a ending terminus. 33: Identified residue LYS10 as a starting terminus. 33: Identified residue MET12 as a ending terminus. 33: Identified residue ASN13 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus ILE-9: COO- 33: Start terminus LYS-10: NH3+ 33: End terminus MET-12: COO- 33: Start terminus ASN-13: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 258 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2 (144 ms) 33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 10 donors and 12 acceptors were found. 33: There are 13 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 33: SG9 33: HIS8 NE251 1.055 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 115, now 115 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 288 pairs 33: Before cleaning: 293 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 6 cmap torsion pairs 33: There are 293 dihedrals, 23 impropers, 203 angles 33: 285 pairs, 115 bonds and 0 virtual sites 33: Total mass 888.952 a.m.u. 33: Total charge -2.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 60, now 60 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 152 pairs 33: Before cleaning: 152 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 152 dihedrals, 5 impropers, 112 angles 33: 152 pairs, 60 bonds and 0 virtual sites 33: Total mass 391.552 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 83, now 83 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 211 pairs 33: Before cleaning: 216 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 3 cmap torsion pairs 33: There are 216 dihedrals, 18 impropers, 148 angles 33: 211 pairs, 83 bonds and 0 virtual sites 33: Total mass 601.643 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: Now there are 258 atoms and 16 residues 33: Total mass in system 1882.146 a.m.u. 33: Total charge in system 0.000 e 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records only (ignoring chain id). 33: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 33: 33: chain #res #atoms 33: 1 'A' 8 61 33: 2 'B' 3 25 33: 3 'C' 5 41 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (61 atoms, 8 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue ILE9 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus ILE-9: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 8 residues with 114 atoms 33: Chain time... 33: Processing chain 2 'B' (25 atoms, 3 residues) 33: Identified residue LYS10 as a starting terminus. 33: Identified residue MET12 as a ending terminus. 33: Start terminus LYS-10: NH3+ 33: End terminus MET-12: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 61 atoms 33: Chain time... 33: Processing chain 3 'C' (41 atoms, 5 residues) 33: Identified residue ASN13 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ASN-13: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 5 residues with 83 atoms 33: Chain time... 33: Including chain 1 in system: 114 atoms 8 residues 33: Including chain 2 in system: 61 atoms 3 residues 33: Including chain 3 in system: 83 atoms 5 residues 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3 (40 ms) 33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 25 donors and 23 acceptors were found. 33: There are 41 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 HIS8 33: SG9 NE251 33: HIS8 NE251 1.055 33: MET12 SD83 0.763 0.990 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 260, now 260 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 650 pairs 33: Before cleaning: 660 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 8 cmap torsion pairs 33: There are 660 dihedrals, 45 impropers, 466 angles 33: 647 pairs, 260 bonds and 0 virtual sites 33: Total mass 1900.162 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: 33: Merged chains into joint molecule definitions at 3 places. 33: 33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 33: 33: chain #res #atoms 33: 1 'A' 16 127 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (127 atoms, 16 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue GLU5 as a ending terminus. 33: Identified residue PHE6 as a starting terminus. 33: Identified residue ILE9 as a ending terminus. 33: Identified residue LYS10 as a starting terminus. 33: Identified residue MET12 as a ending terminus. 33: Identified residue ASN13 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus GLU-5: COO- 33: Start terminus PHE-6: NH3+ 33: End terminus ILE-9: COO- 33: Start terminus LYS-10: NH3+ 33: End terminus MET-12: COO- 33: Start terminus ASN-13: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 261 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4 (63 ms) 33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 50, now 50 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 123 pairs 33: Before cleaning: 123 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 2 cmap torsion pairs 33: There are 123 dihedrals, 9 impropers, 88 angles 33: 123 pairs, 50 bonds and 0 virtual sites 33: Total mass 434.421 a.m.u. 33: Total charge -2.000 e 33: Writing topology 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 6 donors and 4 acceptors were found. 33: There are 3 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 67, now 67 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 164 pairs 33: Before cleaning: 169 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 2 cmap torsion pairs 33: There are 169 dihedrals, 13 impropers, 118 angles 33: 161 pairs, 67 bonds and 0 virtual sites 33: Total mass 472.547 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 60, now 60 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 152 pairs 33: Before cleaning: 152 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 152 dihedrals, 5 impropers, 112 angles 33: 152 pairs, 60 bonds and 0 virtual sites 33: Total mass 391.552 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 83, now 83 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 211 pairs 33: Before cleaning: 216 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 3 cmap torsion pairs 33: There are 216 dihedrals, 18 impropers, 148 angles 33: 211 pairs, 83 bonds and 0 virtual sites 33: Total mass 601.643 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: Now there are 261 atoms and 16 residues 33: Total mass in system 1900.162 a.m.u. 33: Total charge in system 0.000 e 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: WARNING: Chain identifier 'B' is used in two non-sequential blocks. 33: They will be treated as separate chains unless you reorder your file. 33: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms 33: 33: chain #res #atoms 33: 1 'A' 4 28 33: 2 'B' 4 33 33: 3 'B' 3 25 33: 4 'C' 5 41 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (28 atoms, 4 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue GLU5 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus GLU-5: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 4 residues with 51 atoms 33: Chain time... 33: Processing chain 2 'B' (33 atoms, 4 residues) 33: Identified residue PHE6 as a starting terminus. 33: Identified residue ILE9 as a ending terminus. 33: Start terminus PHE-6: NH3+ 33: End terminus ILE-9: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 4 residues with 66 atoms 33: Chain time... 33: Processing chain 3 'B' (25 atoms, 3 residues) 33: Identified residue LYS10 as a starting terminus. 33: Identified residue MET12 as a ending terminus. 33: Start terminus LYS-10: NH3+ 33: End terminus MET-12: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 61 atoms 33: Chain time... 33: Processing chain 4 'C' (41 atoms, 5 residues) 33: Identified residue ASN13 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ASN-13: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 5 residues with 83 atoms 33: Chain time... 33: Including chain 1 in system: 51 atoms 4 residues 33: Including chain 2 in system: 66 atoms 4 residues 33: Including chain 3 in system: 61 atoms 3 residues 33: Including chain 4 in system: 83 atoms 5 residues 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5 (70 ms) 33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 25 donors and 23 acceptors were found. 33: There are 41 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 HIS8 33: SG9 NE251 33: HIS8 NE251 1.055 33: MET12 SD83 0.763 0.990 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 256, now 256 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 652 pairs 33: Before cleaning: 662 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 12 cmap torsion pairs 33: There are 662 dihedrals, 47 impropers, 460 angles 33: 649 pairs, 256 bonds and 0 virtual sites 33: Total mass 1864.131 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records and chain id changing. 33: 33: Merged chains into joint molecule definitions at 1 places. 33: 33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 33: 33: chain #res #atoms 33: 1 'A' 16 127 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (127 atoms, 16 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue MET12 as a ending terminus. 33: Identified residue ASN13 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus MET-12: COO- 33: Start terminus ASN-13: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 255 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6 (85 ms) 33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 14 donors and 15 acceptors were found. 33: There are 20 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 HIS8 33: SG9 NE251 33: HIS8 NE251 1.055 33: MET12 SD83 0.763 0.990 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 173, now 173 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 441 pairs 33: Before cleaning: 446 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 9 cmap torsion pairs 33: There are 446 dihedrals, 29 impropers, 312 angles 33: 438 pairs, 173 bonds and 0 virtual sites 33: Total mass 1262.488 a.m.u. 33: Total charge -1.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 83, now 83 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 211 pairs 33: Before cleaning: 216 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 3 cmap torsion pairs 33: There are 216 dihedrals, 18 impropers, 148 angles 33: 211 pairs, 83 bonds and 0 virtual sites 33: Total mass 601.643 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: Now there are 255 atoms and 16 residues 33: Total mass in system 1864.131 a.m.u. 33: Total charge in system 0.000 e 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records and chain id changing. 33: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms 33: 33: chain #res #atoms 33: 1 'A' 11 86 33: 2 'C' 5 41 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (86 atoms, 11 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue MET12 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus MET-12: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 11 residues with 172 atoms 33: Chain time... 33: Processing chain 2 'C' (41 atoms, 5 residues) 33: Identified residue ASN13 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ASN-13: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 5 residues with 83 atoms 33: Chain time... 33: Including chain 1 in system: 172 atoms 11 residues 33: Including chain 2 in system: 83 atoms 5 residues 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7 (46 ms) 33: [----------] 8 tests from ChainSep/Pdb2gmxTest (711 ms total) 33: 33: [----------] 4 tests from ChainChanges/Pdb2gmxTest 33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 35, now 35 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 83 pairs 33: Before cleaning: 83 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 83 dihedrals, 6 impropers, 61 angles 33: 83 pairs, 35 bonds and 0 virtual sites 33: Total mass 306.314 a.m.u. 33: Total charge -1.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 58, now 58 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 145 pairs 33: Before cleaning: 150 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 150 dihedrals, 5 impropers, 103 angles 33: 142 pairs, 58 bonds and 0 virtual sites 33: Total mass 404.468 a.m.u. 33: Total charge -0.000 e 33: Writing topology 33: Now there are 93 atoms and 6 residues 33: Total mass in system 710.782 a.m.u. 33: Total charge in system -1.000 e 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/two-fragments.pdb... 33: Read 'Fragments of peptides and ions', 47 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on changing chain id only (ignoring TER records). 33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 33: 33: chain #res #atoms 33: 1 'A' 3 19 33: 2 'B' 3 28 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (19 atoms, 3 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue ASP4 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus ASP-4: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 36 atoms 33: Chain time... 33: Processing chain 2 'B' (28 atoms, 3 residues) 33: Identified residue THR18 as a starting terminus. 33: Identified residue TRP20 as a ending terminus. 33: Start terminus THR-18: NH3+ 33: End terminus TRP-20: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 57 atoms 33: Chain time... 33: Including chain 1 in system: 36 atoms 3 residues 33: Including chain 2 in system: 57 atoms 3 residues 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/two-fragments.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0 (52 ms) 33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 35, now 35 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 83 pairs 33: Before cleaning: 83 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 83 dihedrals, 6 impropers, 61 angles 33: 83 pairs, 35 bonds and 0 virtual sites 33: Total mass 306.314 a.m.u. 33: Total charge -1.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 58, now 58 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 145 pairs 33: Before cleaning: 150 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 150 dihedrals, 5 impropers, 103 angles 33: 142 pairs, 58 bonds and 0 virtual sites 33: Total mass 404.468 a.m.u. 33: Total charge -0.000 e 33: Writing topology 33: Now there are 93 atoms and 6 residues 33: Total mass in system 710.782 a.m.u. 33: Total charge in system -1.000 e 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/two-fragments.pdb... 33: Read 'Fragments of peptides and ions', 47 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records only (ignoring chain id). 33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 33: 33: chain #res #atoms 33: 1 'A' 3 19 33: 2 'B' 3 28 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (19 atoms, 3 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue ASP4 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus ASP-4: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 36 atoms 33: Chain time... 33: Processing chain 2 'B' (28 atoms, 3 residues) 33: Identified residue THR18 as a starting terminus. 33: Identified residue TRP20 as a ending terminus. 33: Start terminus THR-18: NH3+ 33: End terminus TRP-20: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 57 atoms 33: Chain time... 33: Including chain 1 in system: 36 atoms 3 residues 33: Including chain 2 in system: 57 atoms 3 residues 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/two-fragments.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1 (31 ms) 33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 35, now 35 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 83 pairs 33: Before cleaning: 83 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 83 dihedrals, 6 impropers, 61 angles 33: 83 pairs, 35 bonds and 0 virtual sites 33: Total mass 306.314 a.m.u. 33: Total charge -1.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 58, now 58 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 145 pairs 33: Before cleaning: 150 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 150 dihedrals, 5 impropers, 103 angles 33: 142 pairs, 58 bonds and 0 virtual sites 33: Total mass 404.468 a.m.u. 33: Total charge -0.000 e 33: Writing topology 33: Now there are 93 atoms and 6 residues 33: Total mass in system 710.782 a.m.u. 33: Total charge in system -1.000 e 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/two-fragments.pdb... 33: Read 'Fragments of peptides and ions', 47 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 33: 33: chain #res #atoms 33: 1 'A' 3 19 33: 2 'B' 3 28 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (19 atoms, 3 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue ASP4 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus ASP-4: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 36 atoms 33: Chain time... 33: Processing chain 2 'B' (28 atoms, 3 residues) 33: Identified residue THR18 as a starting terminus. 33: Identified residue TRP20 as a ending terminus. 33: Start terminus THR-18: NH3+ 33: End terminus TRP-20: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 57 atoms 33: Chain time... 33: Including chain 1 in system: 36 atoms 3 residues 33: Including chain 2 in system: 57 atoms 3 residues 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/two-fragments.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2 (32 ms) 33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 35, now 35 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 83 pairs 33: Before cleaning: 83 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 83 dihedrals, 6 impropers, 61 angles 33: 83 pairs, 35 bonds and 0 virtual sites 33: Total mass 306.314 a.m.u. 33: Total charge -1.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 58, now 58 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 145 pairs 33: Before cleaning: 150 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 150 dihedrals, 5 impropers, 103 angles 33: 142 pairs, 58 bonds and 0 virtual sites 33: Total mass 404.468 a.m.u. 33: Total charge -0.000 e 33: Writing topology 33: Now there are 93 atoms and 6 residues 33: Total mass in system 710.782 a.m.u. 33: Total charge in system -1.000 e 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/two-fragments.pdb... 33: Read 'Fragments of peptides and ions', 47 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records and chain id changing. 33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 33: 33: chain #res #atoms 33: 1 'A' 3 19 33: 2 'B' 3 28 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (19 atoms, 3 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue ASP4 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus ASP-4: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 36 atoms 33: Chain time... 33: Processing chain 2 'B' (28 atoms, 3 residues) 33: Identified residue THR18 as a starting terminus. 33: Identified residue TRP20 as a ending terminus. 33: Start terminus THR-18: NH3+ 33: End terminus TRP-20: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 57 atoms 33: Chain time... 33: Including chain 1 in system: 36 atoms 3 residues 33: Including chain 2 in system: 57 atoms 3 residues 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/two-fragments.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3 (54 ms) 33: [----------] 4 tests from ChainChanges/Pdb2gmxTest (169 ms total) 33: 33: [----------] Global test environment tear-down 33: [==========] 28 tests from 4 test cases ran. (2880 ms total) 33: [ PASSED ] 28 tests. 33/54 Test #33: Pdb2gmx3Test ........................ Passed 2.89 sec test 34 Start 34: CorrelationsTest 34: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/correlations-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/CorrelationsTest.xml" 34: Test timeout computed to be: 30 34: [==========] Running 21 tests from 3 test cases. 34: [----------] Global test environment set-up. 34: [----------] 10 tests from AutocorrTest 34: [ RUN ] AutocorrTest.EacNormal 34: [ OK ] AutocorrTest.EacNormal (368 ms) 34: [ RUN ] AutocorrTest.EacNoNormalize 34: [ OK ] AutocorrTest.EacNoNormalize (200 ms) 34: [ RUN ] AutocorrTest.EacCos 34: [ OK ] AutocorrTest.EacCos (408 ms) 34: [ RUN ] AutocorrTest.EacVector 34: [ OK ] AutocorrTest.EacVector (705 ms) 34: [ RUN ] AutocorrTest.EacRcross 34: [ OK ] AutocorrTest.EacRcross (87 ms) 34: [ RUN ] AutocorrTest.EacP0 34: [ OK ] AutocorrTest.EacP0 (614 ms) 34: [ RUN ] AutocorrTest.EacP1 34: [ OK ] AutocorrTest.EacP1 (703 ms) 34: [ RUN ] AutocorrTest.EacP2 34: [ OK ] AutocorrTest.EacP2 (1301 ms) 34: [ RUN ] AutocorrTest.EacP3 34: [ OK ] AutocorrTest.EacP3 (100 ms) 34: [ RUN ] AutocorrTest.EacP4 34: [ OK ] AutocorrTest.EacP4 (607 ms) 34: [----------] 10 tests from AutocorrTest (5180 ms total) 34: 34: [----------] 1 test from ManyAutocorrelationTest 34: [ RUN ] ManyAutocorrelationTest.Empty 34: [ OK ] ManyAutocorrelationTest.Empty (0 ms) 34: [----------] 1 test from ManyAutocorrelationTest (0 ms total) 34: 34: [----------] 10 tests from ExpfitTest 34: [ RUN ] ExpfitTest.EffnEXP1 34: [ OK ] ExpfitTest.EffnEXP1 (82 ms) 34: [ RUN ] ExpfitTest.EffnEXP2 34: [ OK ] ExpfitTest.EffnEXP2 (3 ms) 34: [ RUN ] ExpfitTest.EffnEXPEXP 34: [ OK ] ExpfitTest.EffnEXPEXP (2 ms) 34: [ RUN ] ExpfitTest.EffnEXP5 34: [ OK ] ExpfitTest.EffnEXP5 (5 ms) 34: [ RUN ] ExpfitTest.EffnEXP7 34: [ OK ] ExpfitTest.EffnEXP7 (4 ms) 34: [ RUN ] ExpfitTest.EffnEXP9 34: [ OK ] ExpfitTest.EffnEXP9 (98 ms) 34: [ RUN ] ExpfitTest.EffnERF 34: [ OK ] ExpfitTest.EffnERF (3 ms) 34: [ RUN ] ExpfitTest.EffnERREST 34: [ OK ] ExpfitTest.EffnERREST (1 ms) 34: [ RUN ] ExpfitTest.EffnVAC 34: [ OK ] ExpfitTest.EffnVAC (6 ms) 34: [ RUN ] ExpfitTest.EffnPRES 34: [ OK ] ExpfitTest.EffnPRES (15 ms) 34: [----------] 10 tests from ExpfitTest (219 ms total) 34: 34: [----------] Global test environment tear-down 34: [==========] 21 tests from 3 test cases ran. (5408 ms total) 34: [ PASSED ] 21 tests. 34/54 Test #34: CorrelationsTest .................... Passed 5.58 sec test 35 Start 35: AnalysisDataUnitTests 35: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/analysisdata-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/AnalysisDataUnitTests.xml" 35: Test timeout computed to be: 30 35: [==========] Running 69 tests from 14 test cases. 35: [----------] Global test environment set-up. 35: [----------] 3 tests from AnalysisDataInitializationTest 35: [ RUN ] AnalysisDataInitializationTest.BasicInitialization 35: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms) 35: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules 35: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms) 35: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules 35: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) 35: [----------] 3 tests from AnalysisDataInitializationTest (0 ms total) 35: 35: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = (anonymous namespace)::SimpleInputData 35: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (1 ms) 35: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (0 ms) 35: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly 35: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (1 ms) 35: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (0 ms) 35: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames 35: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (1 ms) 35: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks 35: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (1 ms) 35: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData 35: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (0 ms) 35: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks 35: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (0 ms) 35: [----------] 8 tests from AnalysisDataCommonTest/0 (4 ms total) 35: 35: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = (anonymous namespace)::DataSetsInputData 35: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (1 ms) 35: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (0 ms) 35: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly 35: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (1 ms) 35: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (1 ms) 35: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames 35: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 35: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks 35: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (1 ms) 35: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData 35: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (0 ms) 35: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks 35: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (0 ms) 35: [----------] 8 tests from AnalysisDataCommonTest/1 (4 ms total) 35: 35: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = (anonymous namespace)::MultipointInputData 35: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (1 ms) 35: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (0 ms) 35: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly 35: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (1 ms) 35: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (1 ms) 35: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames 35: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (1 ms) 35: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks 35: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (0 ms) 35: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData 35: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (0 ms) 35: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks 35: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (1 ms) 35: [----------] 8 tests from AnalysisDataCommonTest/2 (5 ms total) 35: 35: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = (anonymous namespace)::MultipointDataSetsInputData 35: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (1 ms) 35: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (0 ms) 35: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly 35: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (1 ms) 35: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (1 ms) 35: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames 35: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (1 ms) 35: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks 35: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (0 ms) 35: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData 35: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (1 ms) 35: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks 35: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (0 ms) 35: [----------] 8 tests from AnalysisDataCommonTest/3 (5 ms total) 35: 35: [----------] 4 tests from AnalysisArrayDataTest 35: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly 35: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (1 ms) 35: [ RUN ] AnalysisArrayDataTest.StorageWorks 35: [ OK ] AnalysisArrayDataTest.StorageWorks (0 ms) 35: [ RUN ] AnalysisArrayDataTest.CanSetXAxis 35: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) 35: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount 35: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms) 35: [----------] 4 tests from AnalysisArrayDataTest (1 ms total) 35: 35: [----------] 6 tests from AverageModuleTest 35: [ RUN ] AverageModuleTest.BasicTest 35: [ OK ] AverageModuleTest.BasicTest (2 ms) 35: [ RUN ] AverageModuleTest.HandlesMultipointData 35: [ OK ] AverageModuleTest.HandlesMultipointData (1 ms) 35: [ RUN ] AverageModuleTest.HandlesMultipleDataSets 35: [ OK ] AverageModuleTest.HandlesMultipleDataSets (2 ms) 35: [ RUN ] AverageModuleTest.HandlesDataSetAveraging 35: [ OK ] AverageModuleTest.HandlesDataSetAveraging (1 ms) 35: [ RUN ] AverageModuleTest.CanCustomizeXAxis 35: [ OK ] AverageModuleTest.CanCustomizeXAxis (1 ms) 35: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis 35: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (1 ms) 35: [----------] 6 tests from AverageModuleTest (9 ms total) 35: 35: [----------] 2 tests from FrameAverageModuleTest 35: [ RUN ] FrameAverageModuleTest.BasicTest 35: [ OK ] FrameAverageModuleTest.BasicTest (1 ms) 35: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets 35: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (1 ms) 35: [----------] 2 tests from FrameAverageModuleTest (2 ms total) 35: 35: [----------] 7 tests from AnalysisHistogramSettingsTest 35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins 35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) 35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins 35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) 35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount 35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) 35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth 35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) 35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins 35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) 35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins 35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) 35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange 35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) 35: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total) 35: 35: [----------] 2 tests from SimpleHistogramModuleTest 35: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly 35: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (1 ms) 35: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll 35: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (1 ms) 35: [----------] 2 tests from SimpleHistogramModuleTest (2 ms total) 35: 35: [----------] 3 tests from WeightedHistogramModuleTest 35: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly 35: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (1 ms) 35: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll 35: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (1 ms) 35: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets 35: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (1 ms) 35: [----------] 3 tests from WeightedHistogramModuleTest (4 ms total) 35: 35: [----------] 3 tests from BinAverageModuleTest 35: [ RUN ] BinAverageModuleTest.ComputesCorrectly 35: [ OK ] BinAverageModuleTest.ComputesCorrectly (1 ms) 35: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll 35: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (1 ms) 35: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets 35: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (1 ms) 35: [----------] 3 tests from BinAverageModuleTest (3 ms total) 35: 35: [----------] 4 tests from AbstractAverageHistogramTest 35: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly 35: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (1 ms) 35: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram 35: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (1 ms) 35: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth 35: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (1 ms) 35: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins 35: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (1 ms) 35: [----------] 4 tests from AbstractAverageHistogramTest (4 ms total) 35: 35: [----------] 3 tests from LifetimeModuleTest 35: [ RUN ] LifetimeModuleTest.BasicTest 35: [ OK ] LifetimeModuleTest.BasicTest (0 ms) 35: [ RUN ] LifetimeModuleTest.CumulativeTest 35: [ OK ] LifetimeModuleTest.CumulativeTest (0 ms) 35: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets 35: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (1 ms) 35: [----------] 3 tests from LifetimeModuleTest (2 ms total) 35: 35: [----------] Global test environment tear-down 35: [==========] 69 tests from 14 test cases ran. (45 ms total) 35: [ PASSED ] 69 tests. 35/54 Test #35: AnalysisDataUnitTests ............... Passed 0.10 sec test 36 Start 36: CoordinateIOTests 36: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/coordinateio-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/CoordinateIOTests.xml" 36: Test timeout computed to be: 30 36: [==========] Running 64 tests from 19 test cases. 36: [----------] Global test environment set-up. 36: [----------] 1 test from OutputSelectorDeathTest 36: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (10 ms) 36: [----------] 1 test from OutputSelectorDeathTest (10 ms total) 36: 36: [----------] 5 tests from TrajectoryFrameWriterTest 36: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (9 ms) 36: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (9 ms) 36: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (9 ms) 36: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (39 ms) 36: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks 36: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms) 36: [----------] 5 tests from TrajectoryFrameWriterTest (67 ms total) 36: 36: [----------] 5 tests from OutputAdapterContainer 36: [ RUN ] OutputAdapterContainer.MakeEmpty 36: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms) 36: [ RUN ] OutputAdapterContainer.AddAdapter 36: [ OK ] OutputAdapterContainer.AddAdapter (0 ms) 36: [ RUN ] OutputAdapterContainer.RejectBadAdapter 36: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms) 36: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter 36: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms) 36: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters 36: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms) 36: [----------] 5 tests from OutputAdapterContainer (0 ms total) 36: 36: [----------] 5 tests from FlagTest 36: [ RUN ] FlagTest.CanSetSimpleFlag 36: [ OK ] FlagTest.CanSetSimpleFlag (0 ms) 36: [ RUN ] FlagTest.CanAddNewBox 36: [ OK ] FlagTest.CanAddNewBox (0 ms) 36: [ RUN ] FlagTest.SetsImplicitPrecisionChange 36: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms) 36: [ RUN ] FlagTest.SetsImplicitStartTimeChange 36: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms) 36: [ RUN ] FlagTest.SetsImplicitTimeStepChange 36: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms) 36: [----------] 5 tests from FlagTest (0 ms total) 36: 36: [----------] 5 tests from SetAtomsTest 36: [ RUN ] SetAtomsTest.RemovesExistingAtoms 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] SetAtomsTest.RemovesExistingAtoms (6 ms) 36: [ RUN ] SetAtomsTest.AddsNewAtoms 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] SetAtomsTest.AddsNewAtoms (5 ms) 36: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (6 ms) 36: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (5 ms) 36: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (7 ms) 36: [----------] 5 tests from SetAtomsTest (29 ms total) 36: 36: [----------] 2 tests from SetBothTimeTest 36: [ RUN ] SetBothTimeTest.StartTimeZeroWorks 36: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms) 36: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks 36: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms) 36: [----------] 2 tests from SetBothTimeTest (0 ms total) 36: 36: [----------] 2 tests from SetStartTimeTest 36: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart 36: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms) 36: [ RUN ] SetStartTimeTest.WorksWithZeroStart 36: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms) 36: [----------] 2 tests from SetStartTimeTest (0 ms total) 36: 36: [----------] 1 test from SetTimeStepTest 36: [ RUN ] SetTimeStepTest.SetTimeStepWorks 36: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms) 36: [----------] 1 test from SetTimeStepTest (0 ms total) 36: 36: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest 36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (8 ms) 36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (7 ms) 36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (8 ms) 36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (8 ms) 36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (7 ms) 36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (32 ms) 36: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (70 ms total) 36: 36: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles 36: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (7 ms) 36: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (6 ms) 36: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (6 ms) 36: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (19 ms total) 36: 36: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles 36: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 36: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms) 36: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 36: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms) 36: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 36: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms) 36: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total) 36: 36: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles 36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (11 ms) 36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (12 ms) 36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (14 ms) 36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (15 ms) 36: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (52 ms total) 36: 36: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles 36: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (28 ms) 36: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (6 ms) 36: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (6 ms) 36: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (40 ms total) 36: 36: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles 36: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 36: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms) 36: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 36: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms) 36: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 36: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms) 36: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (0 ms total) 36: 36: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles 36: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (7 ms) 36: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (6 ms) 36: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (13 ms total) 36: 36: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles 36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms) 36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms) 36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms) 36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms) 36: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (0 ms total) 36: 36: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles 36: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (6 ms) 36: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (7 ms) 36: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (14 ms total) 36: 36: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles 36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms) 36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms) 36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms) 36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms) 36: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (0 ms total) 36: 36: [----------] 4 tests from ModuleSupported/NoOptionalOutput 36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (6 ms) 36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (7 ms) 36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (7 ms) 36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (7 ms) 36: [----------] 4 tests from ModuleSupported/NoOptionalOutput (27 ms total) 36: 36: [----------] Global test environment tear-down 36: [==========] 64 tests from 19 test cases ran. (342 ms total) 36: [ PASSED ] 64 tests. 36/54 Test #36: CoordinateIOTests ................... Passed 0.37 sec test 37 Start 37: TrajectoryAnalysisUnitTests 37: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/trajectoryanalysis-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" 37: Test timeout computed to be: 30 37: [==========] Running 82 tests from 16 test cases. 37: [----------] Global test environment set-up. 37: [----------] 5 tests from ClustsizeTest 37: [ RUN ] ClustsizeTest.NoMolDefaultCutoff 37: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 37: There is one group in the index 37: '', 24 atoms 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Total number of atoms in clusters = 24 37: cmid: 2, cmax: 4, max_size: 6 37: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 37: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (3 ms) 37: [ RUN ] ClustsizeTest.NoMolShortCutoff 37: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 37: There is one group in the index 37: '', 24 atoms 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Total number of atoms in clusters = 24 37: cmid: 1, cmax: 6, max_size: 6 37: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 37: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (4 ms) 37: [ RUN ] ClustsizeTest.MolDefaultCutoff 37: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: '', 24 atoms 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Total number of atoms in clusters = 8 37: cmid: 2, cmax: 4, max_size: 2 37: 50%100%cmid: 2, cmax: 6, max_size: 2 37: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (3 ms) 37: [ RUN ] ClustsizeTest.MolShortCutoff 37: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: '', 24 atoms 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Total number of atoms in clusters = 8 37: cmid: 1, cmax: 6, max_size: 2 37: 50%100%cmid: 2, cmax: 6, max_size: 2 37: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (2 ms) 37: [ RUN ] ClustsizeTest.MolCSize 37: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: '', 24 atoms 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Total number of atoms in clusters = 8 37: cmid: 2, cmax: 4, max_size: 2 37: 50%100%cmid: 2, cmax: 6, max_size: 2 37: 50%100%[ OK ] ClustsizeTest.MolCSize (3 ms) 37: [----------] 5 tests from ClustsizeTest (15 ms total) 37: 37: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest 37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp 37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (1 ms) 37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory 37: Reading frames from gro file 'Test system', 8 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (3 ms) 37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset 37: Reading frames from gro file 'Test system', 8 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (3 ms) 37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory 37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (1 ms) 37: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (8 ms total) 37: 37: [----------] 11 tests from AngleModuleTest 37: [ RUN ] AngleModuleTest.ComputesSimpleAngles 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.ComputesSimpleAngles (3 ms) 37: [ RUN ] AngleModuleTest.ComputesDihedrals 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.ComputesDihedrals (3 ms) 37: [ RUN ] AngleModuleTest.ComputesVectorPairAngles 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.ComputesVectorPairAngles (3 ms) 37: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (3 ms) 37: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (3 ms) 37: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (3 ms) 37: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles 37: Reading frames from gro file 'Test system for different angles', 33 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (3 ms) 37: [ RUN ] AngleModuleTest.ComputesMultipleAngles 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.ComputesMultipleAngles (3 ms) 37: [ RUN ] AngleModuleTest.HandlesDynamicSelections 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.HandlesDynamicSelections (3 ms) 37: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (36 ms) 37: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (5 ms) 37: [----------] 11 tests from AngleModuleTest (68 ms total) 37: 37: [----------] 4 tests from ConvertTrjModuleTest 37: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput 37: Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 37: Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: Analyzed 1 frames, last time 0.000 37: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (12 ms) 37: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset 37: Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 37: Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: Analyzed 1 frames, last time 0.000 37: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (12 ms) 37: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding 37: Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (3 ms) 37: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection 37: Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (2 ms) 37: [----------] 4 tests from ConvertTrjModuleTest (29 ms total) 37: 37: [----------] 3 tests from DistanceModuleTest 37: [ RUN ] DistanceModuleTest.ComputesDistances 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: atomname S1 S2: 37: Number of samples: 5 37: Average distance: 1.43246 nm 37: Standard deviation: 0.96700 nm 37: [ OK ] DistanceModuleTest.ComputesDistances (5 ms) 37: [ RUN ] DistanceModuleTest.ComputesMultipleDistances 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: atomname S1 S2: 37: Number of samples: 5 37: Average distance: 1.43246 nm 37: Standard deviation: 0.96700 nm 37: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: 37: Number of samples: 4 37: Average distance: 1.81066 nm 37: Standard deviation: 0.79289 nm 37: [ OK ] DistanceModuleTest.ComputesMultipleDistances (4 ms) 37: [ RUN ] DistanceModuleTest.HandlesDynamicSelections 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: atomname S1 S2 and res_cog x < 2.8: 37: Number of samples: 3 37: Average distance: 1.72076 nm 37: Standard deviation: 1.24839 nm 37: [ OK ] DistanceModuleTest.HandlesDynamicSelections (4 ms) 37: [----------] 3 tests from DistanceModuleTest (13 ms total) 37: 37: [----------] 2 tests from ExtractClusterModuleTest 37: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms 37: trr version: GMX_trn_file (single precision) 37: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 37: Analyzed 26 frames, last time 0.050 37: There are 8 clusters containing 26 structures, highest framenr is 25 37: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (4 ms) 37: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset 37: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 37: Analyzed 26 frames, last time 0.050 37: There are 8 clusters containing 26 structures, highest framenr is 25 37: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (4 ms) 37: [----------] 2 tests from ExtractClusterModuleTest (8 ms total) 37: 37: [----------] 2 tests from FreeVolumeModuleTest 37: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume 37: Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 37: Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 37: from the source below. This means the results may be different 37: compared to previous GROMACS versions. 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: A. Bondi 37: van der Waals Volumes and Radii 37: J. Phys. Chem. 68 (1964) pp. 441-451 37: -------- -------- --- Thank You --- -------- -------- 37: 37: Could not determine VDW radius for CO2-RM. Set to zero. 37: Could not determine VDW radius for CO2-RM. Set to zero. 37: Could not determine VDW radius for CO2-RM. Set to zero. 37: Could not determine VDW radius for CO2-RM. Set to zero. 37: Could not determine VDW radius for CO2-RM. Set to zero. 37: Could not determine VDW radius for CO2-RM. Set to zero. 37: Could not determine VDW radius for CO2-RM. Set to zero. 37: Could not determine VDW radius for CO2-RM. Set to zero. 37: Could not determine VDW radius for CO2-RM. Set to zero. 37: Could not determine VDW radius for 40 particles. These were set to zero. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: Analyzed 1 frames, last time 0.000 37: cutoff = 0.18 nm 37: probe_radius = 0 nm 37: seed = 13 37: ninsert = 1000 probes per nm^3 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: A. Bondi 37: van der Waals Volumes and Radii 37: J. Phys. Chem. 68 (1964) pp. 441-451 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David 37: van der Spoel and Luciano T. Costa 37: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 37: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 37: Environ. Sci. Technol. 47 (2013) pp. 7421-7429 37: -------- -------- --- Thank You --- -------- -------- 37: 37: Free volume 38.02 +/- 0.00 % 37: Total volume 68.92 +/- 0.00 nm^3 37: Number of molecules 340 total mass 63491.38 Dalton 37: Average molar mass: 186.74 Dalton 37: Density rho: 1529.71 +/- 0.00 nm^3 37: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 37: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 37: Fractional free volume 0.194 +/- 0.000 37: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (164 ms) 37: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection 37: Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 37: Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 37: from the source below. This means the results may be different 37: compared to previous GROMACS versions. 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: A. Bondi 37: van der Waals Volumes and Radii 37: J. Phys. Chem. 68 (1964) pp. 441-451 37: -------- -------- --- Thank You --- -------- -------- 37: 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: Analyzed 1 frames, last time 0.000 37: cutoff = 0.18 nm 37: probe_radius = 0 nm 37: seed = 17 37: ninsert = 1000 probes per nm^3 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: A. Bondi 37: van der Waals Volumes and Radii 37: J. Phys. Chem. 68 (1964) pp. 441-451 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David 37: van der Spoel and Luciano T. Costa 37: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 37: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 37: Environ. Sci. Technol. 47 (2013) pp. 7421-7429 37: -------- -------- --- Thank You --- -------- -------- 37: 37: Free volume 38.48 +/- 0.00 % 37: Total volume 68.92 +/- 0.00 nm^3 37: Number of molecules 340 total mass 63491.38 Dalton 37: Average molar mass: 186.74 Dalton 37: Density rho: 1529.71 +/- 0.00 nm^3 37: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 37: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 37: Fractional free volume 0.200 +/- 0.000 37: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (150 ms) 37: [----------] 2 tests from FreeVolumeModuleTest (314 ms total) 37: 37: [----------] 9 tests from PairDistanceModuleTest 37: [ RUN ] PairDistanceModuleTest.ComputesAllDistances 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] PairDistanceModuleTest.ComputesAllDistances (3 ms) 37: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (33 ms) 37: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (6 ms) 37: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (5 ms) 37: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (6 ms) 37: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (5 ms) 37: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (6 ms) 37: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (5 ms) 37: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (5 ms) 37: [----------] 9 tests from PairDistanceModuleTest (74 ms total) 37: 37: [----------] 5 tests from RdfModuleTest 37: [ RUN ] RdfModuleTest.BasicTest 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] RdfModuleTest.BasicTest (57 ms) 37: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork 37: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: Analyzed 1 frames, last time 0.000 37: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (21 ms) 37: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (22 ms) 37: [ RUN ] RdfModuleTest.CalculatesSurf 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] RdfModuleTest.CalculatesSurf (13 ms) 37: [ RUN ] RdfModuleTest.CalculatesXY 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] RdfModuleTest.CalculatesXY (48 ms) 37: [----------] 5 tests from RdfModuleTest (161 ms total) 37: 37: [----------] 5 tests from SasaModuleTest 37: [ RUN ] SasaModuleTest.BasicTest 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 37: Michael Scharf 37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 37: of Surface Area and Volume and to Dot Surface Contouring of Molecular 37: Assemblies 37: J. Comp. Chem. 16 (1995) pp. 273-284 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 37: from the source below. This means the results may be different 37: compared to previous GROMACS versions. 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: A. Bondi 37: van der Waals Volumes and Radii 37: J. Phys. Chem. 68 (1964) pp. 441-451 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: [ OK ] SasaModuleTest.BasicTest (13 ms) 37: [ RUN ] SasaModuleTest.HandlesSelectedResidues 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 37: Michael Scharf 37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 37: of Surface Area and Volume and to Dot Surface Contouring of Molecular 37: Assemblies 37: J. Comp. Chem. 16 (1995) pp. 273-284 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 37: from the source below. This means the results may be different 37: compared to previous GROMACS versions. 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: A. Bondi 37: van der Waals Volumes and Radii 37: J. Phys. Chem. 68 (1964) pp. 441-451 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: [ OK ] SasaModuleTest.HandlesSelectedResidues (6 ms) 37: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 37: Michael Scharf 37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 37: of Surface Area and Volume and to Dot Surface Contouring of Molecular 37: Assemblies 37: J. Comp. Chem. 16 (1995) pp. 273-284 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 37: from the source below. This means the results may be different 37: compared to previous GROMACS versions. 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: A. Bondi 37: van der Waals Volumes and Radii 37: J. Phys. Chem. 68 (1964) pp. 441-451 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (6 ms) 37: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 37: Michael Scharf 37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 37: of Surface Area and Volume and to Dot Surface Contouring of Molecular 37: Assemblies 37: J. Comp. Chem. 16 (1995) pp. 273-284 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 37: from the source below. This means the results may be different 37: compared to previous GROMACS versions. 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: A. Bondi 37: van der Waals Volumes and Radii 37: J. Phys. Chem. 68 (1964) pp. 441-451 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (7 ms) 37: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 37: Michael Scharf 37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 37: of Surface Area and Volume and to Dot Surface Contouring of Molecular 37: Assemblies 37: J. Comp. Chem. 16 (1995) pp. 273-284 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 37: from the source below. This means the results may be different 37: compared to previous GROMACS versions. 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: A. Bondi 37: van der Waals Volumes and Radii 37: J. Phys. Chem. 68 (1964) pp. 441-451 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (7 ms) 37: [----------] 5 tests from SasaModuleTest (41 ms total) 37: 37: [----------] 8 tests from SelectModuleTest 37: [ RUN ] SelectModuleTest.BasicTest 37: Reading frames from gro file 'Test system', 15 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] SelectModuleTest.BasicTest (5 ms) 37: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput 37: Reading frames from gro file 'Test system', 15 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (4 ms) 37: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput 37: Reading frames from gro file 'Test system', 15 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (3 ms) 37: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput 37: Reading frames from gro file 'Test system', 15 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (3 ms) 37: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput 37: Reading frames from gro file 'Test system', 15 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (3 ms) 37: [ RUN ] SelectModuleTest.NormalizesSizes 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] SelectModuleTest.NormalizesSizes (2 ms) 37: [ RUN ] SelectModuleTest.WritesResidueNumbers 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] SelectModuleTest.WritesResidueNumbers (2 ms) 37: [ RUN ] SelectModuleTest.WritesResidueIndices 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] SelectModuleTest.WritesResidueIndices (2 ms) 37: [----------] 8 tests from SelectModuleTest (24 ms total) 37: 37: [----------] 10 tests from SurfaceAreaTest 37: [ RUN ] SurfaceAreaTest.ComputesSinglePoint 37: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms) 37: [ RUN ] SurfaceAreaTest.ComputesTwoPoints 37: [ OK ] SurfaceAreaTest.ComputesTwoPoints (1 ms) 37: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius 37: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (1 ms) 37: [ RUN ] SurfaceAreaTest.SurfacePoints12 37: [ OK ] SurfaceAreaTest.SurfacePoints12 (0 ms) 37: [ RUN ] SurfaceAreaTest.SurfacePoints32 37: [ OK ] SurfaceAreaTest.SurfacePoints32 (1 ms) 37: [ RUN ] SurfaceAreaTest.SurfacePoints42 37: [ OK ] SurfaceAreaTest.SurfacePoints42 (0 ms) 37: [ RUN ] SurfaceAreaTest.SurfacePoints122 37: [ OK ] SurfaceAreaTest.SurfacePoints122 (1 ms) 37: [ RUN ] SurfaceAreaTest.Computes100Points 37: [ OK ] SurfaceAreaTest.Computes100Points (0 ms) 37: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC 37: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (27 ms) 37: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC 37: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (4 ms) 37: [----------] 10 tests from SurfaceAreaTest (35 ms total) 37: 37: [----------] 4 tests from TopologyInformation 37: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile 37: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms) 37: [ RUN ] TopologyInformation.WorksWithGroFile 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] TopologyInformation.WorksWithGroFile (3 ms) 37: [ RUN ] TopologyInformation.WorksWithPdbFile 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] TopologyInformation.WorksWithPdbFile (4 ms) 37: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile 37: 37: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to -1214283777 37: Generated 330891 of the 330891 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 330891 of the 330891 1-4 parameter combinations 37: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 37: 37: NOTE 2 [file lysozyme.top, line 1465]: 37: System has non-zero total charge: 2.000000 37: Total charge should normally be an integer. See 37: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 37: for discussion on how close it should be to an integer. 37: 37: 37: 37: Number of degrees of freedom in T-Coupling group rest is 465.00 37: 37: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 37: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 37: Analysing residue names: 37: There are: 10 Protein residues 37: Analysing Protein... 37: This run will generate roughly 0 Mb of data 37: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (558 ms) 37: [----------] 4 tests from TopologyInformation (565 ms total) 37: 37: [----------] 4 tests from TrajectoryModuleTest 37: [ RUN ] TrajectoryModuleTest.BasicTest 37: Reading frames from gro file 'Test system', 15 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] TrajectoryModuleTest.BasicTest (2 ms) 37: [ RUN ] TrajectoryModuleTest.PlotsXOnly 37: Reading frames from gro file 'Test system', 15 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] TrajectoryModuleTest.PlotsXOnly (2 ms) 37: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities 37: Reading frames from gro file 'Test system', 15 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (2 ms) 37: [ RUN ] TrajectoryModuleTest.HandlesNoForces 37: Reading frames from gro file 'Test system', 15 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] TrajectoryModuleTest.HandlesNoForces (24 ms) 37: [----------] 4 tests from TrajectoryModuleTest (31 ms total) 37: 37: [----------] 5 tests from UnionFinderTest 37: [ RUN ] UnionFinderTest.WorksEmpty 37: [ OK ] UnionFinderTest.WorksEmpty (0 ms) 37: [ RUN ] UnionFinderTest.BasicMerges 37: [ OK ] UnionFinderTest.BasicMerges (0 ms) 37: [ RUN ] UnionFinderTest.LargerMerges 37: [ OK ] UnionFinderTest.LargerMerges (0 ms) 37: [ RUN ] UnionFinderTest.LongRightMerge 37: [ OK ] UnionFinderTest.LongRightMerge (0 ms) 37: [ RUN ] UnionFinderTest.LongLeftMerge 37: [ OK ] UnionFinderTest.LongLeftMerge (0 ms) 37: [----------] 5 tests from UnionFinderTest (0 ms total) 37: 37: [----------] 1 test from MappedUnionFinderTest 37: [ RUN ] MappedUnionFinderTest.BasicMerges 37: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) 37: [----------] 1 test from MappedUnionFinderTest (0 ms total) 37: 37: [----------] Global test environment tear-down 37: [==========] 82 tests from 16 test cases ran. (1387 ms total) 37: [ PASSED ] 82 tests. 37/54 Test #37: TrajectoryAnalysisUnitTests ......... Passed 1.43 sec test 38 Start 38: EnergyAnalysisUnitTests 38: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/energyanalysis-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/EnergyAnalysisUnitTests.xml" 38: Test timeout computed to be: 30 38: [==========] Running 7 tests from 4 test cases. 38: [----------] Global test environment set-up. 38: [----------] 1 test from DhdlTest 38: [ RUN ] DhdlTest.ExtractDhdl 38: Opened /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file 38: Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) 38: Note: file tpx version 110, software tpx version 119 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Reading energy frame 6 time 0.060 Reading energy frame 7 time 0.070 Reading energy frame 8 time 0.080 Reading energy frame 9 time 0.090 Reading energy frame 10 time 0.100 Reading energy frame 11 time 0.110 Reading energy frame 12 time 0.120 Reading energy frame 13 time 0.130 Reading energy frame 14 time 0.140 Reading energy frame 15 time 0.150 Reading energy frame 16 time 0.160 Reading energy frame 17 time 0.170 Reading energy frame 18 time 0.180 Reading energy frame 19 time 0.190 Reading energy frame 20 time 0.200 Reading energy frame 30 time 0.300 Reading energy frame 40 time 0.400 Reading energy frame 50 time 0.500 Reading energy frame 60 time 0.600 Reading energy frame 70 time 0.700 Reading energy frame 80 time 0.800 Reading energy frame 90 time 0.900 Reading energy frame 100 time 1.000 Last energy frame read 100 time 1.000 38: 38: 38: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg 38: [ OK ] DhdlTest.ExtractDhdl (6 ms) 38: [----------] 1 test from DhdlTest (6 ms total) 38: 38: [----------] 1 test from OriresTest 38: [ RUN ] OriresTest.ExtractOrires 38: Opened /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file 38: Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) 38: Note: file tpx version 111, software tpx version 119 38: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) 38: End your selection with 0 38: Selecting all 7 orientation restraints 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Reading energy frame 3 time 0.006 Reading energy frame 4 time 0.008 Reading energy frame 5 time 0.010 Reading energy frame 6 time 0.012 Reading energy frame 7 time 0.014 Reading energy frame 8 time 0.016 Reading energy frame 9 time 0.018 Reading energy frame 10 time 0.020 Last energy frame read 10 time 0.020 38: [ OK ] OriresTest.ExtractOrires (9 ms) 38: [----------] 1 test from OriresTest (9 ms total) 38: 38: [----------] 3 tests from EnergyTest 38: [ RUN ] EnergyTest.ExtractEnergy 38: Opened /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 38: 38: Select the terms you want from the following list by 38: selecting either (part of) the name or the number or a combination. 38: End your selection with an empty line or a zero. 38: ------------------------------------------------------------------- 38: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 38: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 38: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 38: 13 Box-Z 14 Volume 15 Density 16 pV 38: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 38: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 38: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 38: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 38: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 38: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 38: 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 38: 38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 38: All statistics are over 5001 points 38: 38: Energy Average Err.Est. RMSD Tot-Drift 38: ------------------------------------------------------------------------------- 38: Potential -34142.2 39 228.993 -62.8906 (kJ/mol) 38: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 38: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 38: [ OK ] EnergyTest.ExtractEnergy (3 ms) 38: [ RUN ] EnergyTest.ExtractEnergyByNumber 38: Opened /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 38: 38: Select the terms you want from the following list by 38: selecting either (part of) the name or the number or a combination. 38: End your selection with an empty line or a zero. 38: ------------------------------------------------------------------- 38: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 38: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 38: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 38: 13 Box-Z 14 Volume 15 Density 16 pV 38: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 38: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 38: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 38: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 38: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 38: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 38: 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 38: 38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 38: All statistics are over 5001 points 38: 38: Energy Average Err.Est. RMSD Tot-Drift 38: ------------------------------------------------------------------------------- 38: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) 38: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 38: Pres. DC -268.49 3 8.52175 13.2804 (bar) 38: [ OK ] EnergyTest.ExtractEnergyByNumber (3 ms) 38: [ RUN ] EnergyTest.ExtractEnergyMixed 38: Opened /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 38: 38: Select the terms you want from the following list by 38: selecting either (part of) the name or the number or a combination. 38: End your selection with an empty line or a zero. 38: ------------------------------------------------------------------- 38: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 38: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 38: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 38: 13 Box-Z 14 Volume 15 Density 16 pV 38: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 38: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 38: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 38: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 38: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 38: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 38: 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 38: 38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets 38: All statistics are over 5001 points 38: 38: Energy Average Err.Est. RMSD Tot-Drift 38: ------------------------------------------------------------------------------- 38: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 38: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 38: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) 38: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 38: [ OK ] EnergyTest.ExtractEnergyMixed (3 ms) 38: [----------] 3 tests from EnergyTest (9 ms total) 38: 38: [----------] 2 tests from ViscosityTest 38: [ RUN ] ViscosityTest.EinsteinViscosity 38: Opened /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 38: 38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 38: All statistics are over 5001 points 38: 38: Energy Average Err.Est. RMSD Tot-Drift 38: ------------------------------------------------------------------------------- 38: Pres-XX 20.2092 65 717.193 185.978 (bar) 38: Pres-XY -47.7351 39 372.522 207.456 (bar) 38: Pres-XZ 11.477 31 379.79 6.80818 (bar) 38: Pres-YX -47.7106 39 372.525 207.5 (bar) 38: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 38: Pres-YZ -41.3534 45 401.216 114.663 (bar) 38: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 38: Pres-ZY -41.3119 45 401.196 114.743 (bar) 38: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 38: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 38: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 38: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 38: [ OK ] ViscosityTest.EinsteinViscosity (773 ms) 38: [ RUN ] ViscosityTest.EinsteinViscosityIntegral 38: Opened /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 38: 38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 38: All statistics are over 5001 points 38: 38: Energy Average Err.Est. RMSD Tot-Drift 38: ------------------------------------------------------------------------------- 38: Pres-XX 20.2092 65 717.193 185.978 (bar) 38: Pres-XY -47.7351 39 372.522 207.456 (bar) 38: Pres-XZ 11.477 31 379.79 6.80818 (bar) 38: Pres-YX -47.7106 39 372.525 207.5 (bar) 38: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 38: Pres-YZ -41.3534 45 401.216 114.663 (bar) 38: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 38: Pres-ZY -41.3119 45 401.196 114.743 (bar) 38: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 38: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 38: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 38: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 38: [ OK ] ViscosityTest.EinsteinViscosityIntegral (792 ms) 38: [----------] 2 tests from ViscosityTest (1565 ms total) 38: 38: [----------] Global test environment tear-down 38: [==========] 7 tests from 4 test cases ran. (1590 ms total) 38: [ PASSED ] 7 tests. 38/54 Test #38: EnergyAnalysisUnitTests ............. Passed 1.80 sec test 39 Start 39: ToolUnitTests 39: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/tool-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/ToolUnitTests.xml" 39: Test timeout computed to be: 30 39: [==========] Running 18 tests from 4 test cases. 39: [----------] Global test environment set-up. 39: [----------] 2 tests from DumpTest 39: 39: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 39: For a correct single-point energy evaluation with nsteps = 0, use 39: continuation = yes to avoid constraining the input coordinates. 39: 39: Setting the LD random seed to -1079269633 39: Generated 330891 of the 330891 non-bonded parameter combinations 39: Generating 1-4 interactions: fudge = 0.5 39: Generated 330891 of the 330891 1-4 parameter combinations 39: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 39: 39: NOTE 2 [file lysozyme.top, line 1465]: 39: System has non-zero total charge: 2.000000 39: Total charge should normally be an integer. See 39: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 39: for discussion on how close it should be to an integer. 39: 39: 39: 39: Number of degrees of freedom in T-Coupling group rest is 465.00 39: 39: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 39: NVE simulation with an initial temperature of zero: will use a Verlet 39: buffer of 10%. Check your energy drift! 39: 39: 39: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 39: You are using a plain Coulomb cut-off, which might produce artifacts. 39: You might want to consider using PME electrostatics. 39: 39: 39: 39: There were 4 notes 39: Analysing residue names: 39: There are: 10 Protein residues 39: Analysing Protein... 39: This run will generate roughly 0 Mb of data 39: [ RUN ] DumpTest.WorksWithTpr 39: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 39: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 39: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr: 39: inputrec: 39: integrator = md 39: tinit = 0 39: dt = 0.001 39: nsteps = 0 39: init-step = 0 39: simulation-part = 1 39: comm-mode = Linear 39: nstcomm = 100 39: bd-fric = 0 39: ld-seed = -1079269633 39: emtol = 10 39: emstep = 0.01 39: niter = 20 39: fcstep = 0 39: nstcgsteep = 1000 39: nbfgscorr = 10 39: rtpi = 0.05 39: nstxout = 0 39: nstvout = 0 39: nstfout = 0 39: nstlog = 1000 39: nstcalcenergy = 100 39: nstenergy = 1000 39: nstxout-compressed = 0 39: compressed-x-precision = 1000 39: cutoff-scheme = Verlet 39: nstlist = 10 39: pbc = xyz 39: periodic-molecules = false 39: verlet-buffer-tolerance = -1 39: rlist = 1.1 39: coulombtype = Cut-off 39: coulomb-modifier = Potential-shift 39: rcoulomb-switch = 0 39: rcoulomb = 1 39: epsilon-r = 1 39: epsilon-rf = inf 39: vdw-type = Cut-off 39: vdw-modifier = Potential-shift 39: rvdw-switch = 0 39: rvdw = 1 39: DispCorr = No 39: table-extension = 1 39: fourierspacing = 0.12 39: fourier-nx = 0 39: fourier-ny = 0 39: fourier-nz = 0 39: pme-order = 4 39: ewald-rtol = 1e-05 39: ewald-rtol-lj = 0.001 39: lj-pme-comb-rule = Geometric 39: ewald-geometry = 0 39: epsilon-surface = 0 39: tcoupl = No 39: nsttcouple = -1 39: nh-chain-length = 0 39: print-nose-hoover-chain-variables = false 39: pcoupl = No 39: pcoupltype = Isotropic 39: nstpcouple = -1 39: tau-p = 1 39: compressibility (3x3): 39: compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: ref-p (3x3): 39: ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: refcoord-scaling = No 39: posres-com (3): 39: posres-com[0]= 0.00000e+00 39: posres-com[1]= 0.00000e+00 39: posres-com[2]= 0.00000e+00 39: posres-comB (3): 39: posres-comB[0]= 0.00000e+00 39: posres-comB[1]= 0.00000e+00 39: posres-comB[2]= 0.00000e+00 39: QMMM = false 39: QMconstraints = 0 39: QMMMscheme = 0 39: MMChargeScaleFactor = 1 39: qm-opts: 39: ngQM = 0 39: constraint-algorithm = Lincs 39: continuation = false 39: Shake-SOR = false 39: shake-tol = 0.0001 39: lincs-order = 4 39: lincs-iter = 1 39: lincs-warnangle = 30 39: nwall = 0 39: wall-type = 9-3 39: wall-r-linpot = -1 39: wall-atomtype[0] = -1 39: wall-atomtype[1] = -1 39: wall-density[0] = 0 39: wall-density[1] = 0 39: wall-ewald-zfac = 3 39: pull = false 39: awh = false 39: rotation = false 39: interactiveMD = false 39: disre = No 39: disre-weighting = Conservative 39: disre-mixed = false 39: dr-fc = 1000 39: dr-tau = 0 39: nstdisreout = 100 39: orire-fc = 0 39: orire-tau = 0 39: nstorireout = 100 39: free-energy = no 39: cos-acceleration = 0 39: deform (3x3): 39: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: simulated-tempering = false 39: swapcoords = no 39: userint1 = 0 39: userint2 = 0 39: userint3 = 0 39: userint4 = 0 39: userreal1 = 0 39: userreal2 = 0 39: userreal3 = 0 39: userreal4 = 0 39: applied-forces: 39: electric-field: 39: x: 39: E0 = 0 39: omega = 0 39: t0 = 0 39: sigma = 0 39: y: 39: E0 = 0 39: omega = 0 39: t0 = 0 39: sigma = 0 39: z: 39: E0 = 0 39: omega = 0 39: t0 = 0 39: sigma = 0 39: density-guided-simulation: 39: active = false 39: group = protein 39: similarity-measure = inner-product 39: atom-spreading-weight = unity 39: force-constant = 1e+09 39: gaussian-transform-spreading-width = 0.2 39: gaussian-transform-spreading-range-in-multiples-of-width = 4 39: reference-density-filename = reference.mrc 39: nst = 1 39: normalize-densities = true 39: adaptive-force-scaling = false 39: adaptive-force-scaling-time-constant = 4 39: grpopts: 39: nrdf: 465 39: ref-t: 0 39: tau-t: 0 39: annealing: No 39: annealing-npoints: 0 39: acc: 0 0 0 39: nfreeze: N N N 39: energygrp-flags[ 0]: 0 39: header: 39: bIr = present 39: bBox = present 39: bTop = present 39: bX = present 39: bV = present 39: bF = not present 39: natoms = 156 39: lambda = 0.000000e+00 39: buffer size = 59422 39: topology: 39: name="First 10 residues from 1AKI" 39: #atoms = 156 39: #molblock = 1 39: molblock (0): 39: moltype = 0 "Protein_chain_B" 39: #molecules = 1 39: #posres_xA = 0 39: #posres_xB = 0 39: bIntermolecularInteractions = false 39: ffparams: 39: atnr=10 39: ntypes=212 39: functype[0]=LJ_SR, c6= 3.35274590e-03, c12= 3.95094276e-06 39: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[2]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 39: functype[3]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 39: functype[4]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 39: functype[5]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 39: functype[6]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06 39: functype[7]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07 39: functype[8]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07 39: functype[9]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 39: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[20]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 39: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[22]=LJ_SR, c6= 2.03050394e-03, c12= 3.73260514e-06 39: functype[23]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 39: functype[24]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06 39: functype[25]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 39: functype[26]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06 39: functype[27]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07 39: functype[28]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07 39: functype[29]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 39: functype[30]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 39: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[32]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 39: functype[33]=LJ_SR, c6= 1.22578131e-04, c12= 2.99263014e-08 39: functype[34]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07 39: functype[35]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07 39: functype[36]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07 39: functype[37]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08 39: functype[38]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08 39: functype[39]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06 39: functype[40]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 39: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[42]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06 39: functype[43]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07 39: functype[44]=LJ_SR, c6= 4.88684513e-03, c12= 1.35898972e-05 39: functype[45]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06 39: functype[46]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06 39: functype[47]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07 39: functype[48]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07 39: functype[49]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 39: functype[50]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 39: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[52]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 39: functype[53]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07 39: functype[54]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06 39: functype[55]=LJ_SR, c6= 2.36385735e-03, c12= 1.58990645e-06 39: functype[56]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06 39: functype[57]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07 39: functype[58]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07 39: functype[59]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06 39: functype[60]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06 39: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[62]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06 39: functype[63]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07 39: functype[64]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06 39: functype[65]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06 39: functype[66]=LJ_SR, c6= 2.34487536e-03, c12= 4.69342376e-06 39: functype[67]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07 39: functype[68]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07 39: functype[69]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05 39: functype[70]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07 39: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[72]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07 39: functype[73]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08 39: functype[74]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07 39: functype[75]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07 39: functype[76]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07 39: functype[77]=LJ_SR, c6= 1.00847494e-04, c12= 2.02561683e-08 39: functype[78]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08 39: functype[79]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07 39: functype[80]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07 39: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[82]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07 39: functype[83]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08 39: functype[84]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07 39: functype[85]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07 39: functype[86]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07 39: functype[87]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08 39: functype[88]=LJ_SR, c6= 1.08571716e-04, c12= 1.40867806e-08 39: functype[89]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07 39: functype[90]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 39: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[92]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 39: functype[93]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06 39: functype[94]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 39: functype[95]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06 39: functype[96]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05 39: functype[97]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07 39: functype[98]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07 39: functype[99]=LJ_SR, c6= 1.54830217e-02, c12= 3.37031743e-05 39: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05 39: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05 39: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05 39: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05 39: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05 39: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05 39: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05 39: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05 39: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05 39: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05 39: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05 39: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05 39: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05 39: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05 39: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05 39: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05 39: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02 39: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02 39: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02 39: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02 39: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02 39: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02 39: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02 39: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02 39: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02 39: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02 39: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02 39: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02 39: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 39: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02 39: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02 39: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02 39: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02 39: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02 39: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02 39: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02 39: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02 39: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02 39: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02 39: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02 39: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39319992e+01, phiB= 1.80000000e+02, cpB= 4.39319992e+01, mult=2 39: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400002e+00, phiB= 1.80000000e+02, cpB= 4.18400002e+00, mult=2 39: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60239983e+00, phiB= 1.80000000e+02, cpB= 4.60239983e+00, mult=2 39: functype[143]=RBDIHS, rbcA[0]= 5.46010017e-01, rbcA[1]= 1.63803005e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405008e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 5.46010017e-01, rbcB[1]= 1.63803005e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405008e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[144]=RBDIHS, rbcA[0]= 7.25920022e-01, rbcA[1]= 2.17776990e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 7.25920022e-01, rbcB[1]= 2.17776990e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[145]=RBDIHS, rbcA[0]= 1.27611995e+00, rbcA[1]= 1.16734004e+00, rbcA[2]= 8.95380020e-01, rbcA[3]=-3.33884001e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 1.27611995e+00, rbcB[1]= 1.16734004e+00, rbcB[2]= 8.95380020e-01, rbcB[3]=-3.33884001e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[146]=RBDIHS, rbcA[0]=-6.91824007e+00, rbcA[1]= 4.67562008e+00, rbcA[2]= 2.24261999e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-6.91824007e+00, rbcB[1]= 4.67562008e+00, rbcB[2]= 2.24261999e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[147]=RBDIHS, rbcA[0]= 9.70690012e-01, rbcA[1]= 2.91206002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275003e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 9.70690012e-01, rbcB[1]= 2.91206002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275003e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[148]=RBDIHS, rbcA[0]= 6.27600014e-01, rbcA[1]= 1.88279998e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040006e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 6.27600014e-01, rbcB[1]= 1.88279998e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040006e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[149]=RBDIHS, rbcA[0]=-1.58989996e-01, rbcA[1]=-4.76980001e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35959983e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-1.58989996e-01, rbcB[1]=-4.76980001e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35959983e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654020e+00, rbcA[2]=-1.04934702e+01, rbcA[3]= 6.73623991e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654020e+00, rbcB[2]=-1.04934702e+01, rbcB[3]= 6.73623991e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[151]=RBDIHS, rbcA[0]= 5.00825024e+00, rbcA[1]=-1.69869995e+00, rbcA[2]=-3.72379988e-01, rbcA[3]=-2.93716002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 5.00825024e+00, rbcB[1]=-1.69869995e+00, rbcB[2]=-3.72379988e-01, rbcB[3]=-2.93716002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[152]=RBDIHS, rbcA[0]= 2.92880011e+00, rbcA[1]=-1.46440005e+00, rbcA[2]= 2.09199995e-01, rbcA[3]=-1.67359996e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 2.92880011e+00, rbcB[1]=-1.46440005e+00, rbcB[2]= 2.09199995e-01, rbcB[3]=-1.67359996e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[153]=RBDIHS, rbcA[0]= 5.77183008e+00, rbcA[1]=-2.67147994e+00, rbcA[2]= 9.58140016e-01, rbcA[3]=-4.05847979e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 5.77183008e+00, rbcB[1]=-2.67147994e+00, rbcB[2]= 9.58140016e-01, rbcB[3]=-4.05847979e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[154]=RBDIHS, rbcA[0]= 8.03330004e-01, rbcA[1]= 2.40999007e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 8.03330004e-01, rbcB[1]= 2.40999007e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[155]=RBDIHS, rbcA[0]= 2.05016003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 2.05016003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[156]=RBDIHS, rbcA[0]= 3.02879791e+01, rbcA[1]=-4.81160021e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 3.02879791e+01, rbcB[1]=-4.81160021e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[157]=RBDIHS, rbcA[0]= 2.54763794e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 2.54763794e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[158]=RBDIHS, rbcA[0]= 1.57025499e+01, rbcA[1]= 3.17565594e+01, rbcA[2]=-3.66935992e+00, rbcA[3]=-4.37897491e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 1.57025499e+01, rbcB[1]= 3.17565594e+01, rbcB[2]=-3.66935992e+00, rbcB[3]=-4.37897491e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[159]=RBDIHS, rbcA[0]=-1.03574896e+01, rbcA[1]=-2.95871601e+01, rbcA[2]=-1.16734004e+00, rbcA[3]= 4.11119919e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-1.03574896e+01, rbcB[1]=-2.95871601e+01, rbcB[2]=-1.16734004e+00, rbcB[3]= 4.11119919e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[160]=RBDIHS, rbcA[0]= 4.50198984e+00, rbcA[1]= 7.82410026e-01, rbcA[2]=-1.60247004e+00, rbcA[3]=-3.68192005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 4.50198984e+00, rbcB[1]= 7.82410026e-01, rbcB[2]=-1.60247004e+00, rbcB[3]=-3.68192005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[161]=RBDIHS, rbcA[0]= 4.22589988e-01, rbcA[1]= 2.70705009e+00, rbcA[2]=-3.12964010e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 4.22589988e-01, rbcB[1]= 2.70705009e+00, rbcB[2]=-3.12964010e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[162]=RBDIHS, rbcA[0]=-7.65670002e-01, rbcA[1]= 2.70705009e+00, rbcA[2]= 4.02501011e+00, rbcA[3]=-5.96639013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-7.65670002e-01, rbcB[1]= 2.70705009e+00, rbcB[2]= 4.02501011e+00, rbcB[3]=-5.96639013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[163]=RBDIHS, rbcA[0]= 9.66499984e-01, rbcA[1]= 2.89950991e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86600995e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 9.66499984e-01, rbcB[1]= 2.89950991e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86600995e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[164]=RBDIHS, rbcA[0]=-4.23421001e+00, rbcA[1]= 7.22159004e+00, rbcA[2]= 1.90789998e+00, rbcA[3]=-4.89527988e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-4.23421001e+00, rbcB[1]= 7.22159004e+00, rbcB[2]= 1.90789998e+00, rbcB[3]=-4.89527988e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[165]=RBDIHS, rbcA[0]= 3.03339996e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03339996e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 3.03339996e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03339996e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[166]=RBDIHS, rbcA[0]= 1.02319698e+01, rbcA[1]= 3.52082992e+00, rbcA[2]=-3.97899008e+00, rbcA[3]=-9.77381992e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 1.02319698e+01, rbcB[1]= 3.52082992e+00, rbcB[2]=-3.97899008e+00, rbcB[3]=-9.77381992e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[167]=RBDIHS, rbcA[0]= 5.49777985e+00, rbcA[1]= 1.41838002e+00, rbcA[2]=-6.91615009e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 5.49777985e+00, rbcB[1]= 1.41838002e+00, rbcB[2]=-6.91615009e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[168]=RBDIHS, rbcA[0]=-1.21755004e+00, rbcA[1]=-3.65264010e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-1.21755004e+00, rbcB[1]=-3.65264010e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[169]=RBDIHS, rbcA[0]=-1.26775002e+00, rbcA[1]= 3.02084994e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49781990e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-1.26775002e+00, rbcB[1]= 3.02084994e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49781990e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[170]=RBDIHS, rbcA[0]= 3.80117011e+00, rbcA[1]=-6.95172024e+00, rbcA[2]=-1.01671004e+00, rbcA[3]= 4.16726017e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 3.80117011e+00, rbcB[1]=-6.95172024e+00, rbcB[2]=-1.01671004e+00, rbcB[3]= 4.16726017e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[171]=RBDIHS, rbcA[0]= 3.70279998e-01, rbcA[1]= 1.11085999e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 3.70279998e-01, rbcB[1]= 1.11085999e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[172]=RBDIHS, rbcA[0]= 3.32042198e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042198e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 3.32042198e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042198e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[173]=RBDIHS, rbcA[0]= 1.63176003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 1.63176003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[174]=RBDIHS, rbcA[0]= 3.40787005e+00, rbcA[1]=-2.80537009e+00, rbcA[2]=-3.59820008e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 3.40787005e+00, rbcB[1]=-2.80537009e+00, rbcB[2]=-3.59820008e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[175]=RBDIHS, rbcA[0]=-1.62590199e+01, rbcA[1]= 9.08765030e+00, rbcA[2]= 7.17138004e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-1.62590199e+01, rbcB[1]= 9.08765030e+00, rbcB[2]= 7.17138004e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[176]=RBDIHS, rbcA[0]= 9.45590019e-01, rbcA[1]= 2.83675003e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 9.45590019e-01, rbcB[1]= 2.83675003e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[177]=RBDIHS, rbcA[0]=-1.50624001e+00, rbcA[1]= 5.37225008e+00, rbcA[2]= 1.17989004e+00, rbcA[3]=-5.04589987e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-1.50624001e+00, rbcB[1]= 5.37225008e+00, rbcB[2]= 1.17989004e+00, rbcB[3]=-5.04589987e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[178]=RBDIHS, rbcA[0]= 1.00416005e+00, rbcA[1]= 3.01248002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664019e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 1.00416005e+00, rbcB[1]= 3.01248002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664019e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[179]=RBDIHS, rbcA[0]= 8.79267979e+00, rbcA[1]=-1.18344402e+01, rbcA[2]= 1.07528996e+00, rbcA[3]= 1.96648002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 8.79267979e+00, rbcB[1]=-1.18344402e+01, rbcB[2]= 1.07528996e+00, rbcB[3]= 1.96648002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[180]=RBDIHS, rbcA[0]=-5.77392006e+00, rbcA[1]= 3.38485003e+00, rbcA[2]= 2.38906002e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-5.77392006e+00, rbcB[1]= 3.38485003e+00, rbcB[2]= 2.38906002e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[181]=RBDIHS, rbcA[0]=-9.08345985e+00, rbcA[1]= 9.75708961e+00, rbcA[2]= 3.45180011e+00, rbcA[3]=-4.12542009e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-9.08345985e+00, rbcB[1]= 9.75708961e+00, rbcB[2]= 3.45180011e+00, rbcB[3]=-4.12542009e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[182]=RBDIHS, rbcA[0]=-4.70699996e-01, rbcA[1]=-1.41209996e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88279998e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-4.70699996e-01, rbcB[1]=-1.41209996e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88279998e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[183]=RBDIHS, rbcA[0]= 3.43088007e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088007e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 3.43088007e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088007e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[184]=RBDIHS, rbcA[0]= 2.57315993e+00, rbcA[1]= 3.49781990e+00, rbcA[2]=-1.10038996e+00, rbcA[3]=-4.97059011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 2.57315993e+00, rbcB[1]= 3.49781990e+00, rbcB[2]=-1.10038996e+00, rbcB[3]=-4.97059011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[185]=RBDIHS, rbcA[0]=-8.22160006e-01, rbcA[1]= 1.12758994e+00, rbcA[2]=-3.05440009e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-8.22160006e-01, rbcB[1]= 1.12758994e+00, rbcB[2]=-3.05440009e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[186]=LJ14, c6A= 3.20536114e-04, c12A= 1.71928207e-07, c6B= 3.20536114e-04, c12B= 1.71928207e-07 39: functype[187]=LJ14, c6A= 1.30458479e-03, c12A= 1.92011203e-06, c6B= 1.30458479e-03, c12B= 1.92011203e-06 39: functype[188]=LJ14, c6A= 1.40760513e-03, c12A= 1.25315830e-06, c6B= 1.40760513e-03, c12B= 1.25315830e-06 39: functype[189]=LJ14, c6A= 1.67637295e-03, c12A= 1.97547138e-06, c6B= 1.67637295e-03, c12B= 1.97547138e-06 39: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00 39: functype[191]=LJ14, c6A= 2.49447097e-04, c12A= 1.67110088e-07, c6B= 2.49447097e-04, c12B= 1.67110088e-07 39: functype[192]=LJ14, c6A= 1.01525197e-03, c12A= 1.86630257e-06, c6B= 1.01525197e-03, c12B= 1.86630257e-06 39: functype[193]=LJ14, c6A= 6.12890653e-05, c12A= 1.49631507e-08, c6B= 6.12890653e-05, c12B= 1.49631507e-08 39: functype[194]=LJ14, c6A= 2.69145414e-04, c12A= 1.09064160e-07, c6B= 2.69145414e-04, c12B= 1.09064160e-07 39: functype[195]=LJ14, c6A= 1.09542510e-03, c12A= 1.21804135e-06, c6B= 1.09542510e-03, c12B= 1.21804135e-06 39: functype[196]=LJ14, c6A= 3.86982108e-04, c12A= 3.18863499e-07, c6B= 3.86982108e-04, c12B= 3.18863499e-07 39: functype[197]=LJ14, c6A= 1.57502061e-03, c12A= 3.56110013e-06, c6B= 1.57502061e-03, c12B= 3.56110013e-06 39: functype[198]=LJ14, c6A= 2.44342256e-03, c12A= 6.79494860e-06, c6B= 2.44342256e-03, c12B= 6.79494860e-06 39: functype[199]=LJ14, c6A= 1.40194211e-03, c12A= 2.15310411e-06, c6B= 1.40194211e-03, c12B= 2.15310411e-06 39: functype[200]=LJ14, c6A= 1.09101785e-03, c12A= 2.09276800e-06, c6B= 1.09101785e-03, c12B= 2.09276800e-06 39: functype[201]=LJ14, c6A= 2.68062693e-04, c12A= 1.87387855e-07, c6B= 2.68062693e-04, c12B= 1.87387855e-07 39: functype[202]=LJ14, c6A= 2.26258271e-04, c12A= 1.37484790e-07, c6B= 2.26258271e-04, c12B= 1.37484790e-07 39: functype[203]=LJ14, c6A= 2.43143426e-04, c12A= 1.54167822e-07, c6B= 2.43143426e-04, c12B= 1.54167822e-07 39: functype[204]=LJ14, c6A= 1.17243768e-03, c12A= 2.34671188e-06, c6B= 1.17243768e-03, c12B= 2.34671188e-06 39: functype[205]=LJ14, c6A= 1.69256027e-03, c12A= 3.99321743e-06, c6B= 1.69256027e-03, c12B= 3.99321743e-06 39: functype[206]=LJ14, c6A= 5.04237469e-05, c12A= 1.01280841e-08, c6B= 5.04237469e-05, c12B= 1.01280841e-08 39: functype[207]=LJ14, c6A= 2.34763342e-04, c12A= 1.14652082e-07, c6B= 2.34763342e-04, c12B= 1.14652082e-07 39: functype[208]=LJ14, c6A= 5.76812672e-05, c12A= 1.02660236e-08, c6B= 5.76812672e-05, c12B= 1.02660236e-08 39: functype[209]=LJ14, c6A= 3.60245234e-03, c12A= 5.76973571e-06, c6B= 3.60245234e-03, c12B= 5.76973571e-06 39: functype[210]=LJ14, c6A= 6.88817876e-04, c12A= 5.02148339e-07, c6B= 6.88817876e-04, c12B= 5.02148339e-07 39: functype[211]=LJ14, c6A= 4.34922846e-03, c12A= 1.07007354e-05, c6B= 4.34922846e-03, c12B= 1.07007354e-05 39: reppow = 12 39: fudgeQQ = 0.5 39: cmap 39: atomtypes: 39: atomtype[ 0]={atomnumber= 7} 39: atomtype[ 1]={atomnumber= 1} 39: atomtype[ 2]={atomnumber= 6} 39: atomtype[ 3]={atomnumber= 1} 39: atomtype[ 4]={atomnumber= 6} 39: atomtype[ 5]={atomnumber= 8} 39: atomtype[ 6]={atomnumber= 6} 39: atomtype[ 7]={atomnumber= 1} 39: atomtype[ 8]={atomnumber= 6} 39: atomtype[ 9]={atomnumber= 16} 39: moltype (0): 39: name="Protein_chain_B" 39: atoms: 39: atom (156): 39: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 39: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 39: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 39: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 39: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6} 39: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 39: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 39: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 39: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 39: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 39: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 39: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 39: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 39: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 39: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 39: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6} 39: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 39: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 39: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 39: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 39: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 39: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 39: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6} 39: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8} 39: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7} 39: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1} 39: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6} 39: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 39: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6} 39: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 39: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 39: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 39: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 39: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 39: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 39: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 39: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 39: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 39: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6} 39: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8} 39: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7} 39: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1} 39: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6} 39: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 39: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6} 39: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 39: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 39: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 39: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 39: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 39: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 39: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 39: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 39: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 39: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 39: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 39: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 39: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 39: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6} 39: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8} 39: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7} 39: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1} 39: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6} 39: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 39: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 39: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6} 39: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8} 39: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7} 39: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1} 39: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6} 39: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 39: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6} 39: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 39: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 39: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6} 39: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 39: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 39: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6} 39: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 39: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 39: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7} 39: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1} 39: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6} 39: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 39: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 39: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 39: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 39: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 39: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 39: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6} 39: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8} 39: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7} 39: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1} 39: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6} 39: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 39: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6} 39: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 39: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 39: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16} 39: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1} 39: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6} 39: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8} 39: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7} 39: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1} 39: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6} 39: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 39: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6} 39: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 39: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 39: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6} 39: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 39: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 39: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6} 39: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 39: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 39: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6} 39: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8} 39: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7} 39: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1} 39: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6} 39: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6} 39: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6} 39: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 39: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 39: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6} 39: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8} 39: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7} 39: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1} 39: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6} 39: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 39: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6} 39: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 39: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 39: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 39: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6} 39: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8} 39: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7} 39: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1} 39: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6} 39: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 39: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6} 39: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 39: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 39: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 39: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6} 39: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8} 39: atom (156): 39: atom[0]={name="N"} 39: atom[1]={name="H1"} 39: atom[2]={name="H2"} 39: atom[3]={name="H3"} 39: atom[4]={name="CA"} 39: atom[5]={name="HA"} 39: atom[6]={name="CB"} 39: atom[7]={name="HB1"} 39: atom[8]={name="HB2"} 39: atom[9]={name="CG"} 39: atom[10]={name="HG1"} 39: atom[11]={name="HG2"} 39: atom[12]={name="CD"} 39: atom[13]={name="HD1"} 39: atom[14]={name="HD2"} 39: atom[15]={name="CE"} 39: atom[16]={name="HE1"} 39: atom[17]={name="HE2"} 39: atom[18]={name="NZ"} 39: atom[19]={name="HZ1"} 39: atom[20]={name="HZ2"} 39: atom[21]={name="HZ3"} 39: atom[22]={name="C"} 39: atom[23]={name="O"} 39: atom[24]={name="N"} 39: atom[25]={name="H"} 39: atom[26]={name="CA"} 39: atom[27]={name="HA"} 39: atom[28]={name="CB"} 39: atom[29]={name="HB"} 39: atom[30]={name="CG1"} 39: atom[31]={name="HG11"} 39: atom[32]={name="HG12"} 39: atom[33]={name="HG13"} 39: atom[34]={name="CG2"} 39: atom[35]={name="HG21"} 39: atom[36]={name="HG22"} 39: atom[37]={name="HG23"} 39: atom[38]={name="C"} 39: atom[39]={name="O"} 39: atom[40]={name="N"} 39: atom[41]={name="H"} 39: atom[42]={name="CA"} 39: atom[43]={name="HA"} 39: atom[44]={name="CB"} 39: atom[45]={name="HB1"} 39: atom[46]={name="HB2"} 39: atom[47]={name="CG"} 39: atom[48]={name="CD1"} 39: atom[49]={name="HD1"} 39: atom[50]={name="CD2"} 39: atom[51]={name="HD2"} 39: atom[52]={name="CE1"} 39: atom[53]={name="HE1"} 39: atom[54]={name="CE2"} 39: atom[55]={name="HE2"} 39: atom[56]={name="CZ"} 39: atom[57]={name="HZ"} 39: atom[58]={name="C"} 39: atom[59]={name="O"} 39: atom[60]={name="N"} 39: atom[61]={name="H"} 39: atom[62]={name="CA"} 39: atom[63]={name="HA1"} 39: atom[64]={name="HA2"} 39: atom[65]={name="C"} 39: atom[66]={name="O"} 39: atom[67]={name="N"} 39: atom[68]={name="H"} 39: atom[69]={name="CA"} 39: atom[70]={name="HA"} 39: atom[71]={name="CB"} 39: atom[72]={name="HB1"} 39: atom[73]={name="HB2"} 39: atom[74]={name="CG"} 39: atom[75]={name="HG1"} 39: atom[76]={name="HG2"} 39: atom[77]={name="CD"} 39: atom[78]={name="HD1"} 39: atom[79]={name="HD2"} 39: atom[80]={name="NE"} 39: atom[81]={name="HE"} 39: atom[82]={name="CZ"} 39: atom[83]={name="NH1"} 39: atom[84]={name="HH11"} 39: atom[85]={name="HH12"} 39: atom[86]={name="NH2"} 39: atom[87]={name="HH21"} 39: atom[88]={name="HH22"} 39: atom[89]={name="C"} 39: atom[90]={name="O"} 39: atom[91]={name="N"} 39: atom[92]={name="H"} 39: atom[93]={name="CA"} 39: atom[94]={name="HA"} 39: atom[95]={name="CB"} 39: atom[96]={name="HB1"} 39: atom[97]={name="HB2"} 39: atom[98]={name="SG"} 39: atom[99]={name="HG"} 39: atom[100]={name="C"} 39: atom[101]={name="O"} 39: atom[102]={name="N"} 39: atom[103]={name="H"} 39: atom[104]={name="CA"} 39: atom[105]={name="HA"} 39: atom[106]={name="CB"} 39: atom[107]={name="HB1"} 39: atom[108]={name="HB2"} 39: atom[109]={name="CG"} 39: atom[110]={name="HG1"} 39: atom[111]={name="HG2"} 39: atom[112]={name="CD"} 39: atom[113]={name="OE1"} 39: atom[114]={name="OE2"} 39: atom[115]={name="C"} 39: atom[116]={name="O"} 39: atom[117]={name="N"} 39: atom[118]={name="H"} 39: atom[119]={name="CA"} 39: atom[120]={name="HA"} 39: atom[121]={name="CB"} 39: atom[122]={name="HB1"} 39: atom[123]={name="HB2"} 39: atom[124]={name="CG"} 39: atom[125]={name="HG"} 39: atom[126]={name="CD1"} 39: atom[127]={name="HD11"} 39: atom[128]={name="HD12"} 39: atom[129]={name="HD13"} 39: atom[130]={name="CD2"} 39: atom[131]={name="HD21"} 39: atom[132]={name="HD22"} 39: atom[133]={name="HD23"} 39: atom[134]={name="C"} 39: atom[135]={name="O"} 39: atom[136]={name="N"} 39: atom[137]={name="H"} 39: atom[138]={name="CA"} 39: atom[139]={name="HA"} 39: atom[140]={name="CB"} 39: atom[141]={name="HB1"} 39: atom[142]={name="HB2"} 39: atom[143]={name="HB3"} 39: atom[144]={name="C"} 39: atom[145]={name="O"} 39: atom[146]={name="N"} 39: atom[147]={name="H"} 39: atom[148]={name="CA"} 39: atom[149]={name="HA"} 39: atom[150]={name="CB"} 39: atom[151]={name="HB1"} 39: atom[152]={name="HB2"} 39: atom[153]={name="HB3"} 39: atom[154]={name="C"} 39: atom[155]={name="O"} 39: type (156): 39: type[0]={name="opls_287",nameB="opls_287"} 39: type[1]={name="opls_290",nameB="opls_290"} 39: type[2]={name="opls_290",nameB="opls_290"} 39: type[3]={name="opls_290",nameB="opls_290"} 39: type[4]={name="opls_293B",nameB="opls_293B"} 39: type[5]={name="opls_140",nameB="opls_140"} 39: type[6]={name="opls_136",nameB="opls_136"} 39: type[7]={name="opls_140",nameB="opls_140"} 39: type[8]={name="opls_140",nameB="opls_140"} 39: type[9]={name="opls_136",nameB="opls_136"} 39: type[10]={name="opls_140",nameB="opls_140"} 39: type[11]={name="opls_140",nameB="opls_140"} 39: type[12]={name="opls_136",nameB="opls_136"} 39: type[13]={name="opls_140",nameB="opls_140"} 39: type[14]={name="opls_140",nameB="opls_140"} 39: type[15]={name="opls_292",nameB="opls_292"} 39: type[16]={name="opls_140",nameB="opls_140"} 39: type[17]={name="opls_140",nameB="opls_140"} 39: type[18]={name="opls_287",nameB="opls_287"} 39: type[19]={name="opls_290",nameB="opls_290"} 39: type[20]={name="opls_290",nameB="opls_290"} 39: type[21]={name="opls_290",nameB="opls_290"} 39: type[22]={name="opls_235",nameB="opls_235"} 39: type[23]={name="opls_236",nameB="opls_236"} 39: type[24]={name="opls_238",nameB="opls_238"} 39: type[25]={name="opls_241",nameB="opls_241"} 39: type[26]={name="opls_224B",nameB="opls_224B"} 39: type[27]={name="opls_140",nameB="opls_140"} 39: type[28]={name="opls_137",nameB="opls_137"} 39: type[29]={name="opls_140",nameB="opls_140"} 39: type[30]={name="opls_135",nameB="opls_135"} 39: type[31]={name="opls_140",nameB="opls_140"} 39: type[32]={name="opls_140",nameB="opls_140"} 39: type[33]={name="opls_140",nameB="opls_140"} 39: type[34]={name="opls_135",nameB="opls_135"} 39: type[35]={name="opls_140",nameB="opls_140"} 39: type[36]={name="opls_140",nameB="opls_140"} 39: type[37]={name="opls_140",nameB="opls_140"} 39: type[38]={name="opls_235",nameB="opls_235"} 39: type[39]={name="opls_236",nameB="opls_236"} 39: type[40]={name="opls_238",nameB="opls_238"} 39: type[41]={name="opls_241",nameB="opls_241"} 39: type[42]={name="opls_224B",nameB="opls_224B"} 39: type[43]={name="opls_140",nameB="opls_140"} 39: type[44]={name="opls_149",nameB="opls_149"} 39: type[45]={name="opls_140",nameB="opls_140"} 39: type[46]={name="opls_140",nameB="opls_140"} 39: type[47]={name="opls_145",nameB="opls_145"} 39: type[48]={name="opls_145",nameB="opls_145"} 39: type[49]={name="opls_146",nameB="opls_146"} 39: type[50]={name="opls_145",nameB="opls_145"} 39: type[51]={name="opls_146",nameB="opls_146"} 39: type[52]={name="opls_145",nameB="opls_145"} 39: type[53]={name="opls_146",nameB="opls_146"} 39: type[54]={name="opls_145",nameB="opls_145"} 39: type[55]={name="opls_146",nameB="opls_146"} 39: type[56]={name="opls_145",nameB="opls_145"} 39: type[57]={name="opls_146",nameB="opls_146"} 39: type[58]={name="opls_235",nameB="opls_235"} 39: type[59]={name="opls_236",nameB="opls_236"} 39: type[60]={name="opls_238",nameB="opls_238"} 39: type[61]={name="opls_241",nameB="opls_241"} 39: type[62]={name="opls_223B",nameB="opls_223B"} 39: type[63]={name="opls_140",nameB="opls_140"} 39: type[64]={name="opls_140",nameB="opls_140"} 39: type[65]={name="opls_235",nameB="opls_235"} 39: type[66]={name="opls_236",nameB="opls_236"} 39: type[67]={name="opls_238",nameB="opls_238"} 39: type[68]={name="opls_241",nameB="opls_241"} 39: type[69]={name="opls_224B",nameB="opls_224B"} 39: type[70]={name="opls_140",nameB="opls_140"} 39: type[71]={name="opls_136",nameB="opls_136"} 39: type[72]={name="opls_140",nameB="opls_140"} 39: type[73]={name="opls_140",nameB="opls_140"} 39: type[74]={name="opls_308",nameB="opls_308"} 39: type[75]={name="opls_140",nameB="opls_140"} 39: type[76]={name="opls_140",nameB="opls_140"} 39: type[77]={name="opls_307",nameB="opls_307"} 39: type[78]={name="opls_140",nameB="opls_140"} 39: type[79]={name="opls_140",nameB="opls_140"} 39: type[80]={name="opls_303",nameB="opls_303"} 39: type[81]={name="opls_304",nameB="opls_304"} 39: type[82]={name="opls_302",nameB="opls_302"} 39: type[83]={name="opls_300",nameB="opls_300"} 39: type[84]={name="opls_301",nameB="opls_301"} 39: type[85]={name="opls_301",nameB="opls_301"} 39: type[86]={name="opls_300",nameB="opls_300"} 39: type[87]={name="opls_301",nameB="opls_301"} 39: type[88]={name="opls_301",nameB="opls_301"} 39: type[89]={name="opls_235",nameB="opls_235"} 39: type[90]={name="opls_236",nameB="opls_236"} 39: type[91]={name="opls_238",nameB="opls_238"} 39: type[92]={name="opls_241",nameB="opls_241"} 39: type[93]={name="opls_224B",nameB="opls_224B"} 39: type[94]={name="opls_140",nameB="opls_140"} 39: type[95]={name="opls_206",nameB="opls_206"} 39: type[96]={name="opls_140",nameB="opls_140"} 39: type[97]={name="opls_140",nameB="opls_140"} 39: type[98]={name="opls_200",nameB="opls_200"} 39: type[99]={name="opls_204",nameB="opls_204"} 39: type[100]={name="opls_235",nameB="opls_235"} 39: type[101]={name="opls_236",nameB="opls_236"} 39: type[102]={name="opls_238",nameB="opls_238"} 39: type[103]={name="opls_241",nameB="opls_241"} 39: type[104]={name="opls_224B",nameB="opls_224B"} 39: type[105]={name="opls_140",nameB="opls_140"} 39: type[106]={name="opls_136",nameB="opls_136"} 39: type[107]={name="opls_140",nameB="opls_140"} 39: type[108]={name="opls_140",nameB="opls_140"} 39: type[109]={name="opls_274",nameB="opls_274"} 39: type[110]={name="opls_140",nameB="opls_140"} 39: type[111]={name="opls_140",nameB="opls_140"} 39: type[112]={name="opls_271",nameB="opls_271"} 39: type[113]={name="opls_272",nameB="opls_272"} 39: type[114]={name="opls_272",nameB="opls_272"} 39: type[115]={name="opls_235",nameB="opls_235"} 39: type[116]={name="opls_236",nameB="opls_236"} 39: type[117]={name="opls_238",nameB="opls_238"} 39: type[118]={name="opls_241",nameB="opls_241"} 39: type[119]={name="opls_224B",nameB="opls_224B"} 39: type[120]={name="opls_140",nameB="opls_140"} 39: type[121]={name="opls_136",nameB="opls_136"} 39: type[122]={name="opls_140",nameB="opls_140"} 39: type[123]={name="opls_140",nameB="opls_140"} 39: type[124]={name="opls_137",nameB="opls_137"} 39: type[125]={name="opls_140",nameB="opls_140"} 39: type[126]={name="opls_135",nameB="opls_135"} 39: type[127]={name="opls_140",nameB="opls_140"} 39: type[128]={name="opls_140",nameB="opls_140"} 39: type[129]={name="opls_140",nameB="opls_140"} 39: type[130]={name="opls_135",nameB="opls_135"} 39: type[131]={name="opls_140",nameB="opls_140"} 39: type[132]={name="opls_140",nameB="opls_140"} 39: type[133]={name="opls_140",nameB="opls_140"} 39: type[134]={name="opls_235",nameB="opls_235"} 39: type[135]={name="opls_236",nameB="opls_236"} 39: type[136]={name="opls_238",nameB="opls_238"} 39: type[137]={name="opls_241",nameB="opls_241"} 39: type[138]={name="opls_224B",nameB="opls_224B"} 39: type[139]={name="opls_140",nameB="opls_140"} 39: type[140]={name="opls_135",nameB="opls_135"} 39: type[141]={name="opls_140",nameB="opls_140"} 39: type[142]={name="opls_140",nameB="opls_140"} 39: type[143]={name="opls_140",nameB="opls_140"} 39: type[144]={name="opls_235",nameB="opls_235"} 39: type[145]={name="opls_236",nameB="opls_236"} 39: type[146]={name="opls_238",nameB="opls_238"} 39: type[147]={name="opls_241",nameB="opls_241"} 39: type[148]={name="opls_224B",nameB="opls_224B"} 39: type[149]={name="opls_140",nameB="opls_140"} 39: type[150]={name="opls_135",nameB="opls_135"} 39: type[151]={name="opls_140",nameB="opls_140"} 39: type[152]={name="opls_140",nameB="opls_140"} 39: type[153]={name="opls_140",nameB="opls_140"} 39: type[154]={name="opls_235",nameB="opls_235"} 39: type[155]={name="opls_236",nameB="opls_236"} 39: residue (10): 39: residue[0]={name="LYS", nr=1, ic=' '} 39: residue[1]={name="VAL", nr=2, ic=' '} 39: residue[2]={name="PHE", nr=3, ic=' '} 39: residue[3]={name="GLY", nr=4, ic=' '} 39: residue[4]={name="ARG", nr=5, ic=' '} 39: residue[5]={name="CYS", nr=6, ic=' '} 39: residue[6]={name="GLU", nr=7, ic=' '} 39: residue[7]={name="LEU", nr=8, ic=' '} 39: residue[8]={name="ALA", nr=9, ic=' '} 39: residue[9]={name="ALA", nr=10, ic=' '} 39: excls: 39: nr=156 39: nra=1828 39: excls[0][0..12]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 39: excls[1][13..20]={0, 1, 2, 3, 4, 5, 6, 22} 39: excls[2][21..28]={0, 1, 2, 3, 4, 5, 6, 22} 39: excls[3][29..36]={0, 1, 2, 3, 4, 5, 6, 22} 39: excls[4][37..54]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 39: 23, 24, 25, 26} 39: excls[5][55..67]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 39: excls[6][68..86]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 39: 14, 15, 22, 23, 24} 39: excls[7][87..97]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 39: excls[8][98..108]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 39: excls[9][109..125]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 39: 16, 17, 18, 22} 39: excls[10][126..136]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 39: excls[11][137..147]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 39: excls[12][148..164]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 39: 17, 18, 19, 20, 21} 39: excls[13][165..175]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 39: excls[14][176..186]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 39: excls[15][187..200]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 39: 19, 20, 21} 39: excls[16][201..211]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 39: excls[17][212..222]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 39: excls[18][223..233]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 39: excls[19][234..241]={12, 15, 16, 17, 18, 19, 20, 21} 39: excls[20][242..249]={12, 15, 16, 17, 18, 19, 20, 21} 39: excls[21][250..257]={12, 15, 16, 17, 18, 19, 20, 21} 39: excls[22][258..275]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 39: 25, 26, 27, 28, 38} 39: excls[23][276..284]={0, 4, 5, 6, 22, 23, 24, 25, 26} 39: excls[24][285..301]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 39: 30, 34, 38, 39, 40} 39: excls[25][302..310]={4, 22, 23, 24, 25, 26, 27, 28, 38} 39: excls[26][311..332]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42} 39: excls[27][333..344]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 39: 40} 39: excls[28][345..362]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39: 34, 35, 36, 37, 38, 39, 40} 39: excls[29][363..376]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39: 36, 37, 38} 39: excls[30][377..390]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39: 36, 37, 38} 39: excls[31][391..398]={26, 28, 29, 30, 31, 32, 33, 34} 39: excls[32][399..406]={26, 28, 29, 30, 31, 32, 33, 34} 39: excls[33][407..414]={26, 28, 29, 30, 31, 32, 33, 34} 39: excls[34][415..428]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39: 36, 37, 38} 39: excls[35][429..436]={26, 28, 29, 30, 34, 35, 36, 37} 39: excls[36][437..444]={26, 28, 29, 30, 34, 35, 36, 37} 39: excls[37][445..452]={26, 28, 29, 30, 34, 35, 36, 37} 39: excls[38][453..469]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 39: 40, 41, 42, 43, 44, 58} 39: excls[39][470..478]={24, 26, 27, 28, 38, 39, 40, 41, 42} 39: excls[40][479..495]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 39: 45, 46, 47, 58, 59, 60} 39: excls[41][496..504]={26, 38, 39, 40, 41, 42, 43, 44, 58} 39: excls[42][505..522]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 39: 48, 50, 58, 59, 60, 61, 62} 39: excls[43][523..534]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 39: 60} 39: excls[44][535..552]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 39: 50, 51, 52, 54, 58, 59, 60} 39: excls[45][553..562]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 39: excls[46][563..572]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 39: excls[47][573..589]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 39: 52, 53, 54, 55, 56, 58} 39: excls[48][590..603]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 39: 54, 56, 57} 39: excls[49][604..611]={44, 47, 48, 49, 50, 52, 53, 56} 39: excls[50][612..625]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 39: 55, 56, 57} 39: excls[51][626..633]={44, 47, 48, 50, 51, 54, 55, 56} 39: excls[52][634..644]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57} 39: excls[53][645..652]={47, 48, 49, 52, 53, 54, 56, 57} 39: excls[54][653..663]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57} 39: excls[55][664..671]={47, 50, 51, 52, 54, 55, 56, 57} 39: excls[56][672..682]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57} 39: excls[57][683..690]={48, 50, 52, 53, 54, 55, 56, 57} 39: excls[58][691..707]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 39: 60, 61, 62, 63, 64, 65} 39: excls[59][708..716]={40, 42, 43, 44, 58, 59, 60, 61, 62} 39: excls[60][717..730]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64, 39: 65, 66, 67} 39: excls[61][731..739]={42, 58, 59, 60, 61, 62, 63, 64, 65} 39: excls[62][740..752]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 39: 68, 69} 39: excls[63][753..761]={58, 60, 61, 62, 63, 64, 65, 66, 67} 39: excls[64][762..770]={58, 60, 61, 62, 63, 64, 65, 66, 67} 39: excls[65][771..784]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 39: 70, 71, 89} 39: excls[66][785..793]={60, 62, 63, 64, 65, 66, 67, 68, 69} 39: excls[67][794..810]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 39: 72, 73, 74, 89, 90, 91} 39: excls[68][811..819]={62, 65, 66, 67, 68, 69, 70, 71, 89} 39: excls[69][820..838]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 39: 75, 76, 77, 89, 90, 91, 92, 93} 39: excls[70][839..850]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 39: 91} 39: excls[71][851..868]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 39: 77, 78, 79, 80, 89, 90, 91} 39: excls[72][869..879]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 39: excls[73][880..890]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 39: excls[74][891..906]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 39: 79, 80, 81, 82, 89} 39: excls[75][907..917]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 39: excls[76][918..928]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 39: excls[77][929..943]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 39: 81, 82, 83, 86} 39: excls[78][944..953]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 39: excls[79][954..963]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 39: excls[80][964..979]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 39: 84, 85, 86, 87, 88} 39: excls[81][980..988]={74, 77, 78, 79, 80, 81, 82, 83, 86} 39: excls[82][989..1001]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 39: 86, 87, 88} 39: excls[83][1002..1011]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 39: excls[84][1012..1017]={80, 82, 83, 84, 85, 86} 39: excls[85][1018..1023]={80, 82, 83, 84, 85, 86} 39: excls[86][1024..1033]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 39: excls[87][1034..1039]={80, 82, 83, 86, 87, 88} 39: excls[88][1040..1045]={80, 82, 83, 86, 87, 88} 39: excls[89][1046..1062]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 39: 90, 91, 92, 93, 94, 95, 100} 39: excls[90][1063..1071]={67, 69, 70, 71, 89, 90, 91, 92, 93} 39: excls[91][1072..1088]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 39: 95, 96, 97, 98, 100, 101, 102} 39: excls[92][1089..1097]={69, 89, 90, 91, 92, 93, 94, 95, 100} 39: excls[93][1098..1114]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 39: 98, 99, 100, 101, 102, 103, 104} 39: excls[94][1115..1126]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 39: 101, 102} 39: excls[95][1127..1139]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 39: 100, 101, 102} 39: excls[96][1140..1148]={91, 93, 94, 95, 96, 97, 98, 99, 100} 39: excls[97][1149..1157]={91, 93, 94, 95, 96, 97, 98, 99, 100} 39: excls[98][1158..1166]={91, 93, 94, 95, 96, 97, 98, 99, 100} 39: excls[99][1167..1172]={93, 95, 96, 97, 98, 99} 39: excls[100][1173..1189]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 39: 101, 102, 103, 104, 105, 106, 115} 39: excls[101][1190..1198]={91, 93, 94, 95, 100, 101, 102, 103, 104} 39: excls[102][1199..1215]={91, 93, 94, 95, 100, 101, 102, 103, 104, 39: 105, 106, 107, 108, 109, 115, 116, 117} 39: excls[103][1216..1224]={93, 100, 101, 102, 103, 104, 105, 106, 39: 115} 39: excls[104][1225..1243]={93, 100, 101, 102, 103, 104, 105, 106, 39: 107, 108, 109, 110, 111, 112, 115, 116, 117, 118, 119} 39: excls[105][1244..1255]={100, 102, 103, 104, 105, 106, 107, 108, 39: 109, 115, 116, 117} 39: excls[106][1256..1272]={100, 102, 103, 104, 105, 106, 107, 108, 39: 109, 110, 111, 112, 113, 114, 115, 116, 117} 39: excls[107][1273..1283]={102, 104, 105, 106, 107, 108, 109, 110, 39: 111, 112, 115} 39: excls[108][1284..1294]={102, 104, 105, 106, 107, 108, 109, 110, 39: 111, 112, 115} 39: excls[109][1295..1307]={102, 104, 105, 106, 107, 108, 109, 110, 39: 111, 112, 113, 114, 115} 39: excls[110][1308..1317]={104, 106, 107, 108, 109, 110, 111, 112, 39: 113, 114} 39: excls[111][1318..1327]={104, 106, 107, 108, 109, 110, 111, 112, 39: 113, 114} 39: excls[112][1328..1337]={104, 106, 107, 108, 109, 110, 111, 112, 39: 113, 114} 39: excls[113][1338..1344]={106, 109, 110, 111, 112, 113, 114} 39: excls[114][1345..1351]={106, 109, 110, 111, 112, 113, 114} 39: excls[115][1352..1368]={100, 102, 103, 104, 105, 106, 107, 108, 39: 109, 115, 116, 117, 118, 119, 120, 121, 134} 39: excls[116][1369..1377]={102, 104, 105, 106, 115, 116, 117, 118, 39: 119} 39: excls[117][1378..1394]={102, 104, 105, 106, 115, 116, 117, 118, 39: 119, 120, 121, 122, 123, 124, 134, 135, 136} 39: excls[118][1395..1403]={104, 115, 116, 117, 118, 119, 120, 121, 39: 134} 39: excls[119][1404..1422]={104, 115, 116, 117, 118, 119, 120, 121, 39: 122, 123, 124, 125, 126, 130, 134, 135, 136, 137, 138} 39: excls[120][1423..1434]={115, 117, 118, 119, 120, 121, 122, 123, 39: 124, 134, 135, 136} 39: excls[121][1435..1455]={115, 117, 118, 119, 120, 121, 122, 123, 39: 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 39: 136} 39: excls[122][1456..1466]={117, 119, 120, 121, 122, 123, 124, 125, 39: 126, 130, 134} 39: excls[123][1467..1477]={117, 119, 120, 121, 122, 123, 124, 125, 39: 126, 130, 134} 39: excls[124][1478..1494]={117, 119, 120, 121, 122, 123, 124, 125, 39: 126, 127, 128, 129, 130, 131, 132, 133, 134} 39: excls[125][1495..1508]={119, 121, 122, 123, 124, 125, 126, 127, 39: 128, 129, 130, 131, 132, 133} 39: excls[126][1509..1522]={119, 121, 122, 123, 124, 125, 126, 127, 39: 128, 129, 130, 131, 132, 133} 39: excls[127][1523..1530]={121, 124, 125, 126, 127, 128, 129, 130} 39: excls[128][1531..1538]={121, 124, 125, 126, 127, 128, 129, 130} 39: excls[129][1539..1546]={121, 124, 125, 126, 127, 128, 129, 130} 39: excls[130][1547..1560]={119, 121, 122, 123, 124, 125, 126, 127, 39: 128, 129, 130, 131, 132, 133} 39: excls[131][1561..1568]={121, 124, 125, 126, 130, 131, 132, 133} 39: excls[132][1569..1576]={121, 124, 125, 126, 130, 131, 132, 133} 39: excls[133][1577..1584]={121, 124, 125, 126, 130, 131, 132, 133} 39: excls[134][1585..1601]={115, 117, 118, 119, 120, 121, 122, 123, 39: 124, 134, 135, 136, 137, 138, 139, 140, 144} 39: excls[135][1602..1610]={117, 119, 120, 121, 134, 135, 136, 137, 39: 138} 39: excls[136][1611..1627]={117, 119, 120, 121, 134, 135, 136, 137, 39: 138, 139, 140, 141, 142, 143, 144, 145, 146} 39: excls[137][1628..1636]={119, 134, 135, 136, 137, 138, 139, 140, 39: 144} 39: excls[138][1637..1652]={119, 134, 135, 136, 137, 138, 139, 140, 39: 141, 142, 143, 144, 145, 146, 147, 148} 39: excls[139][1653..1664]={134, 136, 137, 138, 139, 140, 141, 142, 39: 143, 144, 145, 146} 39: excls[140][1665..1676]={134, 136, 137, 138, 139, 140, 141, 142, 39: 143, 144, 145, 146} 39: excls[141][1677..1684]={136, 138, 139, 140, 141, 142, 143, 144} 39: excls[142][1685..1692]={136, 138, 139, 140, 141, 142, 143, 144} 39: excls[143][1693..1700]={136, 138, 139, 140, 141, 142, 143, 144} 39: excls[144][1701..1717]={134, 136, 137, 138, 139, 140, 141, 142, 39: 143, 144, 145, 146, 147, 148, 149, 150, 154} 39: excls[145][1718..1726]={136, 138, 139, 140, 144, 145, 146, 147, 39: 148} 39: excls[146][1727..1742]={136, 138, 139, 140, 144, 145, 146, 147, 39: 148, 149, 150, 151, 152, 153, 154, 155} 39: excls[147][1743..1751]={138, 144, 145, 146, 147, 148, 149, 150, 39: 154} 39: excls[148][1752..1764]={138, 144, 145, 146, 147, 148, 149, 150, 39: 151, 152, 153, 154, 155} 39: excls[149][1765..1775]={144, 146, 147, 148, 149, 150, 151, 152, 39: 153, 154, 155} 39: excls[150][1776..1786]={144, 146, 147, 148, 149, 150, 151, 152, 39: 153, 154, 155} 39: excls[151][1787..1794]={146, 148, 149, 150, 151, 152, 153, 154} 39: excls[152][1795..1802]={146, 148, 149, 150, 151, 152, 153, 154} 39: excls[153][1803..1810]={146, 148, 149, 150, 151, 152, 153, 154} 39: excls[154][1811..1821]={144, 146, 147, 148, 149, 150, 151, 152, 39: 153, 154, 155} 39: excls[155][1822..1827]={146, 148, 149, 150, 154, 155} 39: Bond: 39: nr: 468 39: iatoms: 39: 0 type=100 (BONDS) 0 1 39: 1 type=100 (BONDS) 0 2 39: 2 type=100 (BONDS) 0 3 39: 3 type=101 (BONDS) 0 4 39: 4 type=102 (BONDS) 4 5 39: 5 type=103 (BONDS) 4 6 39: 6 type=104 (BONDS) 4 22 39: 7 type=102 (BONDS) 6 7 39: 8 type=102 (BONDS) 6 8 39: 9 type=103 (BONDS) 6 9 39: 10 type=102 (BONDS) 9 10 39: 11 type=102 (BONDS) 9 11 39: 12 type=103 (BONDS) 9 12 39: 13 type=102 (BONDS) 12 13 39: 14 type=102 (BONDS) 12 14 39: 15 type=103 (BONDS) 12 15 39: 16 type=102 (BONDS) 15 16 39: 17 type=102 (BONDS) 15 17 39: 18 type=101 (BONDS) 15 18 39: 19 type=100 (BONDS) 18 19 39: 20 type=100 (BONDS) 18 20 39: 21 type=100 (BONDS) 18 21 39: 22 type=105 (BONDS) 22 23 39: 23 type=106 (BONDS) 22 24 39: 24 type=100 (BONDS) 24 25 39: 25 type=107 (BONDS) 24 26 39: 26 type=102 (BONDS) 26 27 39: 27 type=103 (BONDS) 26 28 39: 28 type=104 (BONDS) 26 38 39: 29 type=102 (BONDS) 28 29 39: 30 type=103 (BONDS) 28 30 39: 31 type=103 (BONDS) 28 34 39: 32 type=102 (BONDS) 30 31 39: 33 type=102 (BONDS) 30 32 39: 34 type=102 (BONDS) 30 33 39: 35 type=102 (BONDS) 34 35 39: 36 type=102 (BONDS) 34 36 39: 37 type=102 (BONDS) 34 37 39: 38 type=105 (BONDS) 38 39 39: 39 type=106 (BONDS) 38 40 39: 40 type=100 (BONDS) 40 41 39: 41 type=107 (BONDS) 40 42 39: 42 type=102 (BONDS) 42 43 39: 43 type=103 (BONDS) 42 44 39: 44 type=104 (BONDS) 42 58 39: 45 type=102 (BONDS) 44 45 39: 46 type=102 (BONDS) 44 46 39: 47 type=108 (BONDS) 44 47 39: 48 type=109 (BONDS) 47 48 39: 49 type=109 (BONDS) 47 50 39: 50 type=110 (BONDS) 48 49 39: 51 type=109 (BONDS) 48 52 39: 52 type=110 (BONDS) 50 51 39: 53 type=109 (BONDS) 50 54 39: 54 type=110 (BONDS) 52 53 39: 55 type=109 (BONDS) 52 56 39: 56 type=110 (BONDS) 54 55 39: 57 type=109 (BONDS) 54 56 39: 58 type=110 (BONDS) 56 57 39: 59 type=105 (BONDS) 58 59 39: 60 type=106 (BONDS) 58 60 39: 61 type=100 (BONDS) 60 61 39: 62 type=107 (BONDS) 60 62 39: 63 type=102 (BONDS) 62 63 39: 64 type=102 (BONDS) 62 64 39: 65 type=104 (BONDS) 62 65 39: 66 type=105 (BONDS) 65 66 39: 67 type=106 (BONDS) 65 67 39: 68 type=100 (BONDS) 67 68 39: 69 type=107 (BONDS) 67 69 39: 70 type=102 (BONDS) 69 70 39: 71 type=103 (BONDS) 69 71 39: 72 type=104 (BONDS) 69 89 39: 73 type=102 (BONDS) 71 72 39: 74 type=102 (BONDS) 71 73 39: 75 type=103 (BONDS) 71 74 39: 76 type=102 (BONDS) 74 75 39: 77 type=102 (BONDS) 74 76 39: 78 type=103 (BONDS) 74 77 39: 79 type=102 (BONDS) 77 78 39: 80 type=102 (BONDS) 77 79 39: 81 type=111 (BONDS) 77 80 39: 82 type=100 (BONDS) 80 81 39: 83 type=112 (BONDS) 80 82 39: 84 type=112 (BONDS) 82 83 39: 85 type=112 (BONDS) 82 86 39: 86 type=100 (BONDS) 83 84 39: 87 type=100 (BONDS) 83 85 39: 88 type=100 (BONDS) 86 87 39: 89 type=100 (BONDS) 86 88 39: 90 type=105 (BONDS) 89 90 39: 91 type=106 (BONDS) 89 91 39: 92 type=100 (BONDS) 91 92 39: 93 type=107 (BONDS) 91 93 39: 94 type=102 (BONDS) 93 94 39: 95 type=103 (BONDS) 93 95 39: 96 type=104 (BONDS) 93 100 39: 97 type=102 (BONDS) 95 96 39: 98 type=102 (BONDS) 95 97 39: 99 type=113 (BONDS) 95 98 39: 100 type=114 (BONDS) 98 99 39: 101 type=105 (BONDS) 100 101 39: 102 type=106 (BONDS) 100 102 39: 103 type=100 (BONDS) 102 103 39: 104 type=107 (BONDS) 102 104 39: 105 type=102 (BONDS) 104 105 39: 106 type=103 (BONDS) 104 106 39: 107 type=104 (BONDS) 104 115 39: 108 type=102 (BONDS) 106 107 39: 109 type=102 (BONDS) 106 108 39: 110 type=103 (BONDS) 106 109 39: 111 type=102 (BONDS) 109 110 39: 112 type=102 (BONDS) 109 111 39: 113 type=104 (BONDS) 109 112 39: 114 type=115 (BONDS) 112 113 39: 115 type=115 (BONDS) 112 114 39: 116 type=105 (BONDS) 115 116 39: 117 type=106 (BONDS) 115 117 39: 118 type=100 (BONDS) 117 118 39: 119 type=107 (BONDS) 117 119 39: 120 type=102 (BONDS) 119 120 39: 121 type=103 (BONDS) 119 121 39: 122 type=104 (BONDS) 119 134 39: 123 type=102 (BONDS) 121 122 39: 124 type=102 (BONDS) 121 123 39: 125 type=103 (BONDS) 121 124 39: 126 type=102 (BONDS) 124 125 39: 127 type=103 (BONDS) 124 126 39: 128 type=103 (BONDS) 124 130 39: 129 type=102 (BONDS) 126 127 39: 130 type=102 (BONDS) 126 128 39: 131 type=102 (BONDS) 126 129 39: 132 type=102 (BONDS) 130 131 39: 133 type=102 (BONDS) 130 132 39: 134 type=102 (BONDS) 130 133 39: 135 type=105 (BONDS) 134 135 39: 136 type=106 (BONDS) 134 136 39: 137 type=100 (BONDS) 136 137 39: 138 type=107 (BONDS) 136 138 39: 139 type=102 (BONDS) 138 139 39: 140 type=103 (BONDS) 138 140 39: 141 type=104 (BONDS) 138 144 39: 142 type=102 (BONDS) 140 141 39: 143 type=102 (BONDS) 140 142 39: 144 type=102 (BONDS) 140 143 39: 145 type=105 (BONDS) 144 145 39: 146 type=106 (BONDS) 144 146 39: 147 type=100 (BONDS) 146 147 39: 148 type=107 (BONDS) 146 148 39: 149 type=102 (BONDS) 148 149 39: 150 type=103 (BONDS) 148 150 39: 151 type=104 (BONDS) 148 154 39: 152 type=102 (BONDS) 150 151 39: 153 type=102 (BONDS) 150 152 39: 154 type=102 (BONDS) 150 153 39: 155 type=105 (BONDS) 154 155 39: G96Bond: 39: nr: 0 39: Morse: 39: nr: 0 39: Cubic Bonds: 39: nr: 0 39: Connect Bonds: 39: nr: 0 39: Harmonic Pot.: 39: nr: 0 39: FENE Bonds: 39: nr: 0 39: Tab. Bonds: 39: nr: 0 39: Tab. Bonds NC: 39: nr: 0 39: Restraint Pot.: 39: nr: 0 39: Angle: 39: nr: 1124 39: iatoms: 39: 0 type=116 (ANGLES) 1 0 2 39: 1 type=116 (ANGLES) 1 0 3 39: 2 type=116 (ANGLES) 1 0 4 39: 3 type=116 (ANGLES) 2 0 3 39: 4 type=116 (ANGLES) 2 0 4 39: 5 type=116 (ANGLES) 3 0 4 39: 6 type=116 (ANGLES) 0 4 5 39: 7 type=117 (ANGLES) 0 4 6 39: 8 type=117 (ANGLES) 0 4 22 39: 9 type=118 (ANGLES) 5 4 6 39: 10 type=116 (ANGLES) 5 4 22 39: 11 type=119 (ANGLES) 6 4 22 39: 12 type=118 (ANGLES) 4 6 7 39: 13 type=118 (ANGLES) 4 6 8 39: 14 type=120 (ANGLES) 4 6 9 39: 15 type=121 (ANGLES) 7 6 8 39: 16 type=118 (ANGLES) 7 6 9 39: 17 type=118 (ANGLES) 8 6 9 39: 18 type=118 (ANGLES) 6 9 10 39: 19 type=118 (ANGLES) 6 9 11 39: 20 type=120 (ANGLES) 6 9 12 39: 21 type=121 (ANGLES) 10 9 11 39: 22 type=118 (ANGLES) 10 9 12 39: 23 type=118 (ANGLES) 11 9 12 39: 24 type=118 (ANGLES) 9 12 13 39: 25 type=118 (ANGLES) 9 12 14 39: 26 type=120 (ANGLES) 9 12 15 39: 27 type=121 (ANGLES) 13 12 14 39: 28 type=118 (ANGLES) 13 12 15 39: 29 type=118 (ANGLES) 14 12 15 39: 30 type=118 (ANGLES) 12 15 16 39: 31 type=118 (ANGLES) 12 15 17 39: 32 type=117 (ANGLES) 12 15 18 39: 33 type=121 (ANGLES) 16 15 17 39: 34 type=116 (ANGLES) 16 15 18 39: 35 type=116 (ANGLES) 17 15 18 39: 36 type=116 (ANGLES) 15 18 19 39: 37 type=116 (ANGLES) 15 18 20 39: 38 type=116 (ANGLES) 15 18 21 39: 39 type=116 (ANGLES) 19 18 20 39: 40 type=116 (ANGLES) 19 18 21 39: 41 type=116 (ANGLES) 20 18 21 39: 42 type=122 (ANGLES) 4 22 23 39: 43 type=123 (ANGLES) 4 22 24 39: 44 type=124 (ANGLES) 23 22 24 39: 45 type=125 (ANGLES) 22 24 25 39: 46 type=126 (ANGLES) 22 24 26 39: 47 type=127 (ANGLES) 25 24 26 39: 48 type=116 (ANGLES) 24 26 27 39: 49 type=128 (ANGLES) 24 26 28 39: 50 type=129 (ANGLES) 24 26 38 39: 51 type=118 (ANGLES) 27 26 28 39: 52 type=116 (ANGLES) 27 26 38 39: 53 type=119 (ANGLES) 28 26 38 39: 54 type=118 (ANGLES) 26 28 29 39: 55 type=120 (ANGLES) 26 28 30 39: 56 type=120 (ANGLES) 26 28 34 39: 57 type=118 (ANGLES) 29 28 30 39: 58 type=118 (ANGLES) 29 28 34 39: 59 type=120 (ANGLES) 30 28 34 39: 60 type=118 (ANGLES) 28 30 31 39: 61 type=118 (ANGLES) 28 30 32 39: 62 type=118 (ANGLES) 28 30 33 39: 63 type=121 (ANGLES) 31 30 32 39: 64 type=121 (ANGLES) 31 30 33 39: 65 type=121 (ANGLES) 32 30 33 39: 66 type=118 (ANGLES) 28 34 35 39: 67 type=118 (ANGLES) 28 34 36 39: 68 type=118 (ANGLES) 28 34 37 39: 69 type=121 (ANGLES) 35 34 36 39: 70 type=121 (ANGLES) 35 34 37 39: 71 type=121 (ANGLES) 36 34 37 39: 72 type=122 (ANGLES) 26 38 39 39: 73 type=123 (ANGLES) 26 38 40 39: 74 type=124 (ANGLES) 39 38 40 39: 75 type=125 (ANGLES) 38 40 41 39: 76 type=126 (ANGLES) 38 40 42 39: 77 type=127 (ANGLES) 41 40 42 39: 78 type=116 (ANGLES) 40 42 43 39: 79 type=128 (ANGLES) 40 42 44 39: 80 type=129 (ANGLES) 40 42 58 39: 81 type=118 (ANGLES) 43 42 44 39: 82 type=116 (ANGLES) 43 42 58 39: 83 type=119 (ANGLES) 44 42 58 39: 84 type=118 (ANGLES) 42 44 45 39: 85 type=118 (ANGLES) 42 44 46 39: 86 type=130 (ANGLES) 42 44 47 39: 87 type=121 (ANGLES) 45 44 46 39: 88 type=116 (ANGLES) 45 44 47 39: 89 type=116 (ANGLES) 46 44 47 39: 90 type=131 (ANGLES) 44 47 48 39: 91 type=131 (ANGLES) 44 47 50 39: 92 type=132 (ANGLES) 48 47 50 39: 93 type=133 (ANGLES) 47 48 49 39: 94 type=132 (ANGLES) 47 48 52 39: 95 type=133 (ANGLES) 49 48 52 39: 96 type=133 (ANGLES) 47 50 51 39: 97 type=132 (ANGLES) 47 50 54 39: 98 type=133 (ANGLES) 51 50 54 39: 99 type=133 (ANGLES) 48 52 53 39: 100 type=132 (ANGLES) 48 52 56 39: 101 type=133 (ANGLES) 53 52 56 39: 102 type=133 (ANGLES) 50 54 55 39: 103 type=132 (ANGLES) 50 54 56 39: 104 type=133 (ANGLES) 55 54 56 39: 105 type=132 (ANGLES) 52 56 54 39: 106 type=133 (ANGLES) 52 56 57 39: 107 type=133 (ANGLES) 54 56 57 39: 108 type=122 (ANGLES) 42 58 59 39: 109 type=123 (ANGLES) 42 58 60 39: 110 type=124 (ANGLES) 59 58 60 39: 111 type=125 (ANGLES) 58 60 61 39: 112 type=126 (ANGLES) 58 60 62 39: 113 type=127 (ANGLES) 61 60 62 39: 114 type=116 (ANGLES) 60 62 63 39: 115 type=116 (ANGLES) 60 62 64 39: 116 type=129 (ANGLES) 60 62 65 39: 117 type=121 (ANGLES) 63 62 64 39: 118 type=116 (ANGLES) 63 62 65 39: 119 type=116 (ANGLES) 64 62 65 39: 120 type=122 (ANGLES) 62 65 66 39: 121 type=123 (ANGLES) 62 65 67 39: 122 type=124 (ANGLES) 66 65 67 39: 123 type=125 (ANGLES) 65 67 68 39: 124 type=126 (ANGLES) 65 67 69 39: 125 type=127 (ANGLES) 68 67 69 39: 126 type=116 (ANGLES) 67 69 70 39: 127 type=128 (ANGLES) 67 69 71 39: 128 type=129 (ANGLES) 67 69 89 39: 129 type=118 (ANGLES) 70 69 71 39: 130 type=116 (ANGLES) 70 69 89 39: 131 type=119 (ANGLES) 71 69 89 39: 132 type=118 (ANGLES) 69 71 72 39: 133 type=118 (ANGLES) 69 71 73 39: 134 type=120 (ANGLES) 69 71 74 39: 135 type=121 (ANGLES) 72 71 73 39: 136 type=118 (ANGLES) 72 71 74 39: 137 type=118 (ANGLES) 73 71 74 39: 138 type=118 (ANGLES) 71 74 75 39: 139 type=118 (ANGLES) 71 74 76 39: 140 type=120 (ANGLES) 71 74 77 39: 141 type=121 (ANGLES) 75 74 76 39: 142 type=118 (ANGLES) 75 74 77 39: 143 type=118 (ANGLES) 76 74 77 39: 144 type=118 (ANGLES) 74 77 78 39: 145 type=118 (ANGLES) 74 77 79 39: 146 type=117 (ANGLES) 74 77 80 39: 147 type=121 (ANGLES) 78 77 79 39: 148 type=116 (ANGLES) 78 77 80 39: 149 type=116 (ANGLES) 79 77 80 39: 150 type=134 (ANGLES) 77 80 81 39: 151 type=135 (ANGLES) 77 80 82 39: 152 type=133 (ANGLES) 81 80 82 39: 153 type=131 (ANGLES) 80 82 83 39: 154 type=131 (ANGLES) 80 82 86 39: 155 type=131 (ANGLES) 83 82 86 39: 156 type=133 (ANGLES) 82 83 84 39: 157 type=133 (ANGLES) 82 83 85 39: 158 type=133 (ANGLES) 84 83 85 39: 159 type=133 (ANGLES) 82 86 87 39: 160 type=133 (ANGLES) 82 86 88 39: 161 type=133 (ANGLES) 87 86 88 39: 162 type=122 (ANGLES) 69 89 90 39: 163 type=123 (ANGLES) 69 89 91 39: 164 type=124 (ANGLES) 90 89 91 39: 165 type=125 (ANGLES) 89 91 92 39: 166 type=126 (ANGLES) 89 91 93 39: 167 type=127 (ANGLES) 92 91 93 39: 168 type=116 (ANGLES) 91 93 94 39: 169 type=128 (ANGLES) 91 93 95 39: 170 type=129 (ANGLES) 91 93 100 39: 171 type=118 (ANGLES) 94 93 95 39: 172 type=116 (ANGLES) 94 93 100 39: 173 type=119 (ANGLES) 95 93 100 39: 174 type=118 (ANGLES) 93 95 96 39: 175 type=118 (ANGLES) 93 95 97 39: 176 type=136 (ANGLES) 93 95 98 39: 177 type=121 (ANGLES) 96 95 97 39: 178 type=116 (ANGLES) 96 95 98 39: 179 type=116 (ANGLES) 97 95 98 39: 180 type=137 (ANGLES) 95 98 99 39: 181 type=122 (ANGLES) 93 100 101 39: 182 type=123 (ANGLES) 93 100 102 39: 183 type=124 (ANGLES) 101 100 102 39: 184 type=125 (ANGLES) 100 102 103 39: 185 type=126 (ANGLES) 100 102 104 39: 186 type=127 (ANGLES) 103 102 104 39: 187 type=116 (ANGLES) 102 104 105 39: 188 type=128 (ANGLES) 102 104 106 39: 189 type=129 (ANGLES) 102 104 115 39: 190 type=118 (ANGLES) 105 104 106 39: 191 type=116 (ANGLES) 105 104 115 39: 192 type=119 (ANGLES) 106 104 115 39: 193 type=118 (ANGLES) 104 106 107 39: 194 type=118 (ANGLES) 104 106 108 39: 195 type=120 (ANGLES) 104 106 109 39: 196 type=121 (ANGLES) 107 106 108 39: 197 type=118 (ANGLES) 107 106 109 39: 198 type=118 (ANGLES) 108 106 109 39: 199 type=118 (ANGLES) 106 109 110 39: 200 type=118 (ANGLES) 106 109 111 39: 201 type=119 (ANGLES) 106 109 112 39: 202 type=121 (ANGLES) 110 109 111 39: 203 type=116 (ANGLES) 110 109 112 39: 204 type=116 (ANGLES) 111 109 112 39: 205 type=138 (ANGLES) 109 112 113 39: 206 type=138 (ANGLES) 109 112 114 39: 207 type=139 (ANGLES) 113 112 114 39: 208 type=122 (ANGLES) 104 115 116 39: 209 type=123 (ANGLES) 104 115 117 39: 210 type=124 (ANGLES) 116 115 117 39: 211 type=125 (ANGLES) 115 117 118 39: 212 type=126 (ANGLES) 115 117 119 39: 213 type=127 (ANGLES) 118 117 119 39: 214 type=116 (ANGLES) 117 119 120 39: 215 type=128 (ANGLES) 117 119 121 39: 216 type=129 (ANGLES) 117 119 134 39: 217 type=118 (ANGLES) 120 119 121 39: 218 type=116 (ANGLES) 120 119 134 39: 219 type=119 (ANGLES) 121 119 134 39: 220 type=118 (ANGLES) 119 121 122 39: 221 type=118 (ANGLES) 119 121 123 39: 222 type=120 (ANGLES) 119 121 124 39: 223 type=121 (ANGLES) 122 121 123 39: 224 type=118 (ANGLES) 122 121 124 39: 225 type=118 (ANGLES) 123 121 124 39: 226 type=118 (ANGLES) 121 124 125 39: 227 type=120 (ANGLES) 121 124 126 39: 228 type=120 (ANGLES) 121 124 130 39: 229 type=118 (ANGLES) 125 124 126 39: 230 type=118 (ANGLES) 125 124 130 39: 231 type=120 (ANGLES) 126 124 130 39: 232 type=118 (ANGLES) 124 126 127 39: 233 type=118 (ANGLES) 124 126 128 39: 234 type=118 (ANGLES) 124 126 129 39: 235 type=121 (ANGLES) 127 126 128 39: 236 type=121 (ANGLES) 127 126 129 39: 237 type=121 (ANGLES) 128 126 129 39: 238 type=118 (ANGLES) 124 130 131 39: 239 type=118 (ANGLES) 124 130 132 39: 240 type=118 (ANGLES) 124 130 133 39: 241 type=121 (ANGLES) 131 130 132 39: 242 type=121 (ANGLES) 131 130 133 39: 243 type=121 (ANGLES) 132 130 133 39: 244 type=122 (ANGLES) 119 134 135 39: 245 type=123 (ANGLES) 119 134 136 39: 246 type=124 (ANGLES) 135 134 136 39: 247 type=125 (ANGLES) 134 136 137 39: 248 type=126 (ANGLES) 134 136 138 39: 249 type=127 (ANGLES) 137 136 138 39: 250 type=116 (ANGLES) 136 138 139 39: 251 type=128 (ANGLES) 136 138 140 39: 252 type=129 (ANGLES) 136 138 144 39: 253 type=118 (ANGLES) 139 138 140 39: 254 type=116 (ANGLES) 139 138 144 39: 255 type=119 (ANGLES) 140 138 144 39: 256 type=118 (ANGLES) 138 140 141 39: 257 type=118 (ANGLES) 138 140 142 39: 258 type=118 (ANGLES) 138 140 143 39: 259 type=121 (ANGLES) 141 140 142 39: 260 type=121 (ANGLES) 141 140 143 39: 261 type=121 (ANGLES) 142 140 143 39: 262 type=122 (ANGLES) 138 144 145 39: 263 type=123 (ANGLES) 138 144 146 39: 264 type=124 (ANGLES) 145 144 146 39: 265 type=125 (ANGLES) 144 146 147 39: 266 type=126 (ANGLES) 144 146 148 39: 267 type=127 (ANGLES) 147 146 148 39: 268 type=116 (ANGLES) 146 148 149 39: 269 type=128 (ANGLES) 146 148 150 39: 270 type=129 (ANGLES) 146 148 154 39: 271 type=118 (ANGLES) 149 148 150 39: 272 type=116 (ANGLES) 149 148 154 39: 273 type=119 (ANGLES) 150 148 154 39: 274 type=118 (ANGLES) 148 150 151 39: 275 type=118 (ANGLES) 148 150 152 39: 276 type=118 (ANGLES) 148 150 153 39: 277 type=121 (ANGLES) 151 150 152 39: 278 type=121 (ANGLES) 151 150 153 39: 279 type=121 (ANGLES) 152 150 153 39: 280 type=122 (ANGLES) 148 154 155 39: G96Angle: 39: nr: 0 39: Restricted Angles: 39: nr: 0 39: Lin. Angle: 39: nr: 0 39: Bond-Cross: 39: nr: 0 39: BA-Cross: 39: nr: 0 39: U-B: 39: nr: 0 39: Quartic Angles: 39: nr: 0 39: Tab. Angles: 39: nr: 0 39: Proper Dih.: 39: nr: 145 39: iatoms: 39: 0 type=140 (PDIHS) 4 24 22 23 39: 1 type=141 (PDIHS) 22 26 24 25 39: 2 type=140 (PDIHS) 26 40 38 39 39: 3 type=141 (PDIHS) 38 42 40 41 39: 4 type=140 (PDIHS) 42 60 58 59 39: 5 type=142 (PDIHS) 44 47 50 48 39: 6 type=142 (PDIHS) 47 52 48 49 39: 7 type=142 (PDIHS) 47 54 50 51 39: 8 type=142 (PDIHS) 48 56 52 53 39: 9 type=142 (PDIHS) 50 56 54 55 39: 10 type=142 (PDIHS) 52 54 56 57 39: 11 type=141 (PDIHS) 58 62 60 61 39: 12 type=140 (PDIHS) 62 67 65 66 39: 13 type=141 (PDIHS) 65 69 67 68 39: 14 type=140 (PDIHS) 69 91 89 90 39: 15 type=141 (PDIHS) 77 82 80 81 39: 16 type=140 (PDIHS) 80 83 82 86 39: 17 type=141 (PDIHS) 82 84 83 85 39: 18 type=141 (PDIHS) 82 87 86 88 39: 19 type=141 (PDIHS) 89 93 91 92 39: 20 type=140 (PDIHS) 93 102 100 101 39: 21 type=141 (PDIHS) 100 104 102 103 39: 22 type=140 (PDIHS) 104 117 115 116 39: 23 type=140 (PDIHS) 109 113 112 114 39: 24 type=141 (PDIHS) 115 119 117 118 39: 25 type=140 (PDIHS) 119 136 134 135 39: 26 type=141 (PDIHS) 134 138 136 137 39: 27 type=140 (PDIHS) 138 146 144 145 39: 28 type=141 (PDIHS) 144 148 146 147 39: Ryckaert-Bell.: 39: nr: 1565 39: iatoms: 39: 0 type=143 (RBDIHS) 1 0 4 5 39: 1 type=144 (RBDIHS) 1 0 4 6 39: 2 type=144 (RBDIHS) 1 0 4 22 39: 3 type=143 (RBDIHS) 2 0 4 5 39: 4 type=144 (RBDIHS) 2 0 4 6 39: 5 type=144 (RBDIHS) 2 0 4 22 39: 6 type=143 (RBDIHS) 3 0 4 5 39: 7 type=144 (RBDIHS) 3 0 4 6 39: 8 type=144 (RBDIHS) 3 0 4 22 39: 9 type=145 (RBDIHS) 0 4 6 9 39: 10 type=146 (RBDIHS) 22 4 6 9 39: 11 type=147 (RBDIHS) 0 4 6 7 39: 12 type=147 (RBDIHS) 0 4 6 8 39: 13 type=148 (RBDIHS) 5 4 6 7 39: 14 type=148 (RBDIHS) 5 4 6 8 39: 15 type=148 (RBDIHS) 5 4 6 9 39: 16 type=149 (RBDIHS) 22 4 6 7 39: 17 type=149 (RBDIHS) 22 4 6 8 39: 18 type=150 (RBDIHS) 0 4 22 24 39: 19 type=151 (RBDIHS) 6 4 22 24 39: 20 type=148 (RBDIHS) 4 6 9 10 39: 21 type=148 (RBDIHS) 4 6 9 11 39: 22 type=152 (RBDIHS) 4 6 9 12 39: 23 type=148 (RBDIHS) 7 6 9 10 39: 24 type=148 (RBDIHS) 7 6 9 11 39: 25 type=148 (RBDIHS) 7 6 9 12 39: 26 type=148 (RBDIHS) 8 6 9 10 39: 27 type=148 (RBDIHS) 8 6 9 11 39: 28 type=148 (RBDIHS) 8 6 9 12 39: 29 type=148 (RBDIHS) 6 9 12 13 39: 30 type=148 (RBDIHS) 6 9 12 14 39: 31 type=152 (RBDIHS) 6 9 12 15 39: 32 type=148 (RBDIHS) 10 9 12 13 39: 33 type=148 (RBDIHS) 10 9 12 14 39: 34 type=148 (RBDIHS) 10 9 12 15 39: 35 type=148 (RBDIHS) 11 9 12 13 39: 36 type=148 (RBDIHS) 11 9 12 14 39: 37 type=148 (RBDIHS) 11 9 12 15 39: 38 type=148 (RBDIHS) 9 12 15 16 39: 39 type=148 (RBDIHS) 9 12 15 17 39: 40 type=153 (RBDIHS) 9 12 15 18 39: 41 type=148 (RBDIHS) 13 12 15 16 39: 42 type=148 (RBDIHS) 13 12 15 17 39: 43 type=154 (RBDIHS) 13 12 15 18 39: 44 type=148 (RBDIHS) 14 12 15 16 39: 45 type=148 (RBDIHS) 14 12 15 17 39: 46 type=154 (RBDIHS) 14 12 15 18 39: 47 type=144 (RBDIHS) 12 15 18 19 39: 48 type=144 (RBDIHS) 12 15 18 20 39: 49 type=144 (RBDIHS) 12 15 18 21 39: 50 type=143 (RBDIHS) 16 15 18 19 39: 51 type=143 (RBDIHS) 16 15 18 20 39: 52 type=143 (RBDIHS) 16 15 18 21 39: 53 type=143 (RBDIHS) 17 15 18 19 39: 54 type=143 (RBDIHS) 17 15 18 20 39: 55 type=143 (RBDIHS) 17 15 18 21 39: 56 type=155 (RBDIHS) 4 22 24 25 39: 57 type=156 (RBDIHS) 4 22 24 26 39: 58 type=155 (RBDIHS) 23 22 24 25 39: 59 type=157 (RBDIHS) 23 22 24 26 39: 60 type=158 (RBDIHS) 22 24 26 28 39: 61 type=159 (RBDIHS) 22 24 26 38 39: 62 type=160 (RBDIHS) 24 26 28 30 39: 63 type=160 (RBDIHS) 24 26 28 34 39: 64 type=161 (RBDIHS) 38 26 28 30 39: 65 type=161 (RBDIHS) 38 26 28 34 39: 66 type=147 (RBDIHS) 24 26 28 29 39: 67 type=148 (RBDIHS) 27 26 28 29 39: 68 type=148 (RBDIHS) 27 26 28 30 39: 69 type=148 (RBDIHS) 27 26 28 34 39: 70 type=149 (RBDIHS) 38 26 28 29 39: 71 type=150 (RBDIHS) 24 26 38 40 39: 72 type=151 (RBDIHS) 28 26 38 40 39: 73 type=148 (RBDIHS) 26 28 30 31 39: 74 type=148 (RBDIHS) 26 28 30 32 39: 75 type=148 (RBDIHS) 26 28 30 33 39: 76 type=148 (RBDIHS) 29 28 30 31 39: 77 type=148 (RBDIHS) 29 28 30 32 39: 78 type=148 (RBDIHS) 29 28 30 33 39: 79 type=148 (RBDIHS) 34 28 30 31 39: 80 type=148 (RBDIHS) 34 28 30 32 39: 81 type=148 (RBDIHS) 34 28 30 33 39: 82 type=148 (RBDIHS) 26 28 34 35 39: 83 type=148 (RBDIHS) 26 28 34 36 39: 84 type=148 (RBDIHS) 26 28 34 37 39: 85 type=148 (RBDIHS) 29 28 34 35 39: 86 type=148 (RBDIHS) 29 28 34 36 39: 87 type=148 (RBDIHS) 29 28 34 37 39: 88 type=148 (RBDIHS) 30 28 34 35 39: 89 type=148 (RBDIHS) 30 28 34 36 39: 90 type=148 (RBDIHS) 30 28 34 37 39: 91 type=155 (RBDIHS) 26 38 40 41 39: 92 type=156 (RBDIHS) 26 38 40 42 39: 93 type=155 (RBDIHS) 39 38 40 41 39: 94 type=157 (RBDIHS) 39 38 40 42 39: 95 type=158 (RBDIHS) 38 40 42 44 39: 96 type=159 (RBDIHS) 38 40 42 58 39: 97 type=147 (RBDIHS) 40 42 44 45 39: 98 type=147 (RBDIHS) 40 42 44 46 39: 99 type=162 (RBDIHS) 40 42 44 47 39: 100 type=148 (RBDIHS) 43 42 44 45 39: 101 type=148 (RBDIHS) 43 42 44 46 39: 102 type=163 (RBDIHS) 43 42 44 47 39: 103 type=149 (RBDIHS) 58 42 44 45 39: 104 type=149 (RBDIHS) 58 42 44 46 39: 105 type=164 (RBDIHS) 58 42 44 47 39: 106 type=150 (RBDIHS) 40 42 58 60 39: 107 type=151 (RBDIHS) 44 42 58 60 39: 108 type=165 (RBDIHS) 44 47 48 49 39: 109 type=165 (RBDIHS) 44 47 48 52 39: 110 type=165 (RBDIHS) 50 47 48 49 39: 111 type=165 (RBDIHS) 50 47 48 52 39: 112 type=165 (RBDIHS) 44 47 50 51 39: 113 type=165 (RBDIHS) 44 47 50 54 39: 114 type=165 (RBDIHS) 48 47 50 51 39: 115 type=165 (RBDIHS) 48 47 50 54 39: 116 type=165 (RBDIHS) 47 48 52 53 39: 117 type=165 (RBDIHS) 47 48 52 56 39: 118 type=165 (RBDIHS) 49 48 52 53 39: 119 type=165 (RBDIHS) 49 48 52 56 39: 120 type=165 (RBDIHS) 47 50 54 55 39: 121 type=165 (RBDIHS) 47 50 54 56 39: 122 type=165 (RBDIHS) 51 50 54 55 39: 123 type=165 (RBDIHS) 51 50 54 56 39: 124 type=165 (RBDIHS) 48 52 56 54 39: 125 type=165 (RBDIHS) 48 52 56 57 39: 126 type=165 (RBDIHS) 53 52 56 54 39: 127 type=165 (RBDIHS) 53 52 56 57 39: 128 type=165 (RBDIHS) 50 54 56 52 39: 129 type=165 (RBDIHS) 50 54 56 57 39: 130 type=165 (RBDIHS) 55 54 56 52 39: 131 type=165 (RBDIHS) 55 54 56 57 39: 132 type=155 (RBDIHS) 42 58 60 61 39: 133 type=156 (RBDIHS) 42 58 60 62 39: 134 type=155 (RBDIHS) 59 58 60 61 39: 135 type=157 (RBDIHS) 59 58 60 62 39: 136 type=159 (RBDIHS) 58 60 62 65 39: 137 type=150 (RBDIHS) 60 62 65 67 39: 138 type=155 (RBDIHS) 62 65 67 68 39: 139 type=156 (RBDIHS) 62 65 67 69 39: 140 type=155 (RBDIHS) 66 65 67 68 39: 141 type=157 (RBDIHS) 66 65 67 69 39: 142 type=158 (RBDIHS) 65 67 69 71 39: 143 type=159 (RBDIHS) 65 67 69 89 39: 144 type=166 (RBDIHS) 67 69 71 74 39: 145 type=167 (RBDIHS) 89 69 71 74 39: 146 type=147 (RBDIHS) 67 69 71 72 39: 147 type=147 (RBDIHS) 67 69 71 73 39: 148 type=148 (RBDIHS) 70 69 71 72 39: 149 type=148 (RBDIHS) 70 69 71 73 39: 150 type=148 (RBDIHS) 70 69 71 74 39: 151 type=149 (RBDIHS) 89 69 71 72 39: 152 type=149 (RBDIHS) 89 69 71 73 39: 153 type=150 (RBDIHS) 67 69 89 91 39: 154 type=151 (RBDIHS) 71 69 89 91 39: 155 type=148 (RBDIHS) 69 71 74 75 39: 156 type=148 (RBDIHS) 69 71 74 76 39: 157 type=152 (RBDIHS) 69 71 74 77 39: 158 type=148 (RBDIHS) 72 71 74 75 39: 159 type=148 (RBDIHS) 72 71 74 76 39: 160 type=148 (RBDIHS) 72 71 74 77 39: 161 type=148 (RBDIHS) 73 71 74 75 39: 162 type=148 (RBDIHS) 73 71 74 76 39: 163 type=148 (RBDIHS) 73 71 74 77 39: 164 type=148 (RBDIHS) 71 74 77 78 39: 165 type=148 (RBDIHS) 71 74 77 79 39: 166 type=153 (RBDIHS) 71 74 77 80 39: 167 type=148 (RBDIHS) 75 74 77 78 39: 168 type=148 (RBDIHS) 75 74 77 79 39: 169 type=168 (RBDIHS) 75 74 77 80 39: 170 type=148 (RBDIHS) 76 74 77 78 39: 171 type=148 (RBDIHS) 76 74 77 79 39: 172 type=168 (RBDIHS) 76 74 77 80 39: 173 type=169 (RBDIHS) 74 77 80 81 39: 174 type=170 (RBDIHS) 74 77 80 82 39: 175 type=171 (RBDIHS) 78 77 80 82 39: 176 type=171 (RBDIHS) 79 77 80 82 39: 177 type=172 (RBDIHS) 77 80 82 83 39: 178 type=172 (RBDIHS) 77 80 82 86 39: 179 type=173 (RBDIHS) 81 80 82 83 39: 180 type=173 (RBDIHS) 81 80 82 86 39: 181 type=173 (RBDIHS) 80 82 83 84 39: 182 type=173 (RBDIHS) 80 82 83 85 39: 183 type=173 (RBDIHS) 86 82 83 84 39: 184 type=173 (RBDIHS) 86 82 83 85 39: 185 type=173 (RBDIHS) 80 82 86 87 39: 186 type=173 (RBDIHS) 80 82 86 88 39: 187 type=173 (RBDIHS) 83 82 86 87 39: 188 type=173 (RBDIHS) 83 82 86 88 39: 189 type=155 (RBDIHS) 69 89 91 92 39: 190 type=156 (RBDIHS) 69 89 91 93 39: 191 type=155 (RBDIHS) 90 89 91 92 39: 192 type=157 (RBDIHS) 90 89 91 93 39: 193 type=158 (RBDIHS) 89 91 93 95 39: 194 type=159 (RBDIHS) 89 91 93 100 39: 195 type=174 (RBDIHS) 91 93 95 98 39: 196 type=175 (RBDIHS) 100 93 95 98 39: 197 type=147 (RBDIHS) 91 93 95 96 39: 198 type=147 (RBDIHS) 91 93 95 97 39: 199 type=148 (RBDIHS) 94 93 95 96 39: 200 type=148 (RBDIHS) 94 93 95 97 39: 201 type=176 (RBDIHS) 94 93 95 98 39: 202 type=149 (RBDIHS) 100 93 95 96 39: 203 type=149 (RBDIHS) 100 93 95 97 39: 204 type=150 (RBDIHS) 91 93 100 102 39: 205 type=151 (RBDIHS) 95 93 100 102 39: 206 type=177 (RBDIHS) 93 95 98 99 39: 207 type=178 (RBDIHS) 96 95 98 99 39: 208 type=178 (RBDIHS) 97 95 98 99 39: 209 type=155 (RBDIHS) 93 100 102 103 39: 210 type=156 (RBDIHS) 93 100 102 104 39: 211 type=155 (RBDIHS) 101 100 102 103 39: 212 type=157 (RBDIHS) 101 100 102 104 39: 213 type=158 (RBDIHS) 100 102 104 106 39: 214 type=159 (RBDIHS) 100 102 104 115 39: 215 type=179 (RBDIHS) 102 104 106 109 39: 216 type=180 (RBDIHS) 115 104 106 109 39: 217 type=147 (RBDIHS) 102 104 106 107 39: 218 type=147 (RBDIHS) 102 104 106 108 39: 219 type=148 (RBDIHS) 105 104 106 107 39: 220 type=148 (RBDIHS) 105 104 106 108 39: 221 type=148 (RBDIHS) 105 104 106 109 39: 222 type=149 (RBDIHS) 115 104 106 107 39: 223 type=149 (RBDIHS) 115 104 106 108 39: 224 type=150 (RBDIHS) 102 104 115 117 39: 225 type=151 (RBDIHS) 106 104 115 117 39: 226 type=148 (RBDIHS) 104 106 109 110 39: 227 type=148 (RBDIHS) 104 106 109 111 39: 228 type=181 (RBDIHS) 104 106 109 112 39: 229 type=148 (RBDIHS) 107 106 109 110 39: 230 type=148 (RBDIHS) 107 106 109 111 39: 231 type=182 (RBDIHS) 107 106 109 112 39: 232 type=148 (RBDIHS) 108 106 109 110 39: 233 type=148 (RBDIHS) 108 106 109 111 39: 234 type=182 (RBDIHS) 108 106 109 112 39: 235 type=183 (RBDIHS) 106 109 112 113 39: 236 type=183 (RBDIHS) 106 109 112 114 39: 237 type=155 (RBDIHS) 104 115 117 118 39: 238 type=156 (RBDIHS) 104 115 117 119 39: 239 type=155 (RBDIHS) 116 115 117 118 39: 240 type=157 (RBDIHS) 116 115 117 119 39: 241 type=158 (RBDIHS) 115 117 119 121 39: 242 type=159 (RBDIHS) 115 117 119 134 39: 243 type=184 (RBDIHS) 117 119 121 124 39: 244 type=185 (RBDIHS) 134 119 121 124 39: 245 type=147 (RBDIHS) 117 119 121 122 39: 246 type=147 (RBDIHS) 117 119 121 123 39: 247 type=148 (RBDIHS) 120 119 121 122 39: 248 type=148 (RBDIHS) 120 119 121 123 39: 249 type=148 (RBDIHS) 120 119 121 124 39: 250 type=149 (RBDIHS) 134 119 121 122 39: 251 type=149 (RBDIHS) 134 119 121 123 39: 252 type=150 (RBDIHS) 117 119 134 136 39: 253 type=151 (RBDIHS) 121 119 134 136 39: 254 type=148 (RBDIHS) 119 121 124 125 39: 255 type=152 (RBDIHS) 119 121 124 126 39: 256 type=152 (RBDIHS) 119 121 124 130 39: 257 type=148 (RBDIHS) 122 121 124 125 39: 258 type=148 (RBDIHS) 122 121 124 126 39: 259 type=148 (RBDIHS) 122 121 124 130 39: 260 type=148 (RBDIHS) 123 121 124 125 39: 261 type=148 (RBDIHS) 123 121 124 126 39: 262 type=148 (RBDIHS) 123 121 124 130 39: 263 type=148 (RBDIHS) 121 124 126 127 39: 264 type=148 (RBDIHS) 121 124 126 128 39: 265 type=148 (RBDIHS) 121 124 126 129 39: 266 type=148 (RBDIHS) 125 124 126 127 39: 267 type=148 (RBDIHS) 125 124 126 128 39: 268 type=148 (RBDIHS) 125 124 126 129 39: 269 type=148 (RBDIHS) 130 124 126 127 39: 270 type=148 (RBDIHS) 130 124 126 128 39: 271 type=148 (RBDIHS) 130 124 126 129 39: 272 type=148 (RBDIHS) 121 124 130 131 39: 273 type=148 (RBDIHS) 121 124 130 132 39: 274 type=148 (RBDIHS) 121 124 130 133 39: 275 type=148 (RBDIHS) 125 124 130 131 39: 276 type=148 (RBDIHS) 125 124 130 132 39: 277 type=148 (RBDIHS) 125 124 130 133 39: 278 type=148 (RBDIHS) 126 124 130 131 39: 279 type=148 (RBDIHS) 126 124 130 132 39: 280 type=148 (RBDIHS) 126 124 130 133 39: 281 type=155 (RBDIHS) 119 134 136 137 39: 282 type=156 (RBDIHS) 119 134 136 138 39: 283 type=155 (RBDIHS) 135 134 136 137 39: 284 type=157 (RBDIHS) 135 134 136 138 39: 285 type=158 (RBDIHS) 134 136 138 140 39: 286 type=159 (RBDIHS) 134 136 138 144 39: 287 type=147 (RBDIHS) 136 138 140 141 39: 288 type=147 (RBDIHS) 136 138 140 142 39: 289 type=147 (RBDIHS) 136 138 140 143 39: 290 type=148 (RBDIHS) 139 138 140 141 39: 291 type=148 (RBDIHS) 139 138 140 142 39: 292 type=148 (RBDIHS) 139 138 140 143 39: 293 type=149 (RBDIHS) 144 138 140 141 39: 294 type=149 (RBDIHS) 144 138 140 142 39: 295 type=149 (RBDIHS) 144 138 140 143 39: 296 type=150 (RBDIHS) 136 138 144 146 39: 297 type=151 (RBDIHS) 140 138 144 146 39: 298 type=155 (RBDIHS) 138 144 146 147 39: 299 type=156 (RBDIHS) 138 144 146 148 39: 300 type=155 (RBDIHS) 145 144 146 147 39: 301 type=157 (RBDIHS) 145 144 146 148 39: 302 type=158 (RBDIHS) 144 146 148 150 39: 303 type=159 (RBDIHS) 144 146 148 154 39: 304 type=147 (RBDIHS) 146 148 150 151 39: 305 type=147 (RBDIHS) 146 148 150 152 39: 306 type=147 (RBDIHS) 146 148 150 153 39: 307 type=148 (RBDIHS) 149 148 150 151 39: 308 type=148 (RBDIHS) 149 148 150 152 39: 309 type=148 (RBDIHS) 149 148 150 153 39: 310 type=149 (RBDIHS) 154 148 150 151 39: 311 type=149 (RBDIHS) 154 148 150 152 39: 312 type=149 (RBDIHS) 154 148 150 153 39: Restricted Dih.: 39: nr: 0 39: CBT Dih.: 39: nr: 0 39: Fourier Dih.: 39: nr: 0 39: Improper Dih.: 39: nr: 0 39: Improper Dih.: 39: nr: 0 39: Tab. Dih.: 39: nr: 0 39: CMAP Dih.: 39: nr: 0 39: GB 1-2 Pol. (unused): 39: nr: 0 39: GB 1-3 Pol. (unused): 39: nr: 0 39: GB 1-4 Pol. (unused): 39: nr: 0 39: GB Polarization (unused): 39: nr: 0 39: Nonpolar Sol. (unused): 39: nr: 0 39: LJ-14: 39: nr: 1197 39: iatoms: 39: 0 type=186 (LJ14) 0 7 39: 1 type=186 (LJ14) 0 8 39: 2 type=187 (LJ14) 0 9 39: 3 type=188 (LJ14) 0 23 39: 4 type=189 (LJ14) 0 24 39: 5 type=190 (LJ14) 1 5 39: 6 type=190 (LJ14) 1 6 39: 7 type=190 (LJ14) 1 22 39: 8 type=190 (LJ14) 2 5 39: 9 type=190 (LJ14) 2 6 39: 10 type=190 (LJ14) 2 22 39: 11 type=190 (LJ14) 3 5 39: 12 type=190 (LJ14) 3 6 39: 13 type=190 (LJ14) 3 22 39: 14 type=191 (LJ14) 4 10 39: 15 type=191 (LJ14) 4 11 39: 16 type=192 (LJ14) 4 12 39: 17 type=190 (LJ14) 4 25 39: 18 type=192 (LJ14) 4 26 39: 19 type=193 (LJ14) 5 7 39: 20 type=193 (LJ14) 5 8 39: 21 type=191 (LJ14) 5 9 39: 22 type=194 (LJ14) 5 23 39: 23 type=186 (LJ14) 5 24 39: 24 type=191 (LJ14) 6 13 39: 25 type=191 (LJ14) 6 14 39: 26 type=192 (LJ14) 6 15 39: 27 type=195 (LJ14) 6 23 39: 28 type=187 (LJ14) 6 24 39: 29 type=193 (LJ14) 7 10 39: 30 type=193 (LJ14) 7 11 39: 31 type=191 (LJ14) 7 12 39: 32 type=196 (LJ14) 7 22 39: 33 type=193 (LJ14) 8 10 39: 34 type=193 (LJ14) 8 11 39: 35 type=191 (LJ14) 8 12 39: 36 type=196 (LJ14) 8 22 39: 37 type=191 (LJ14) 9 16 39: 38 type=191 (LJ14) 9 17 39: 39 type=187 (LJ14) 9 18 39: 40 type=197 (LJ14) 9 22 39: 41 type=193 (LJ14) 10 13 39: 42 type=193 (LJ14) 10 14 39: 43 type=191 (LJ14) 10 15 39: 44 type=193 (LJ14) 11 13 39: 45 type=193 (LJ14) 11 14 39: 46 type=191 (LJ14) 11 15 39: 47 type=190 (LJ14) 12 19 39: 48 type=190 (LJ14) 12 20 39: 49 type=190 (LJ14) 12 21 39: 50 type=193 (LJ14) 13 16 39: 51 type=193 (LJ14) 13 17 39: 52 type=186 (LJ14) 13 18 39: 53 type=193 (LJ14) 14 16 39: 54 type=193 (LJ14) 14 17 39: 55 type=186 (LJ14) 14 18 39: 56 type=190 (LJ14) 16 19 39: 57 type=190 (LJ14) 16 20 39: 58 type=190 (LJ14) 16 21 39: 59 type=190 (LJ14) 17 19 39: 60 type=190 (LJ14) 17 20 39: 61 type=190 (LJ14) 17 21 39: 62 type=196 (LJ14) 22 27 39: 63 type=197 (LJ14) 22 28 39: 64 type=198 (LJ14) 22 38 39: 65 type=190 (LJ14) 23 25 39: 66 type=195 (LJ14) 23 26 39: 67 type=186 (LJ14) 24 29 39: 68 type=187 (LJ14) 24 30 39: 69 type=187 (LJ14) 24 34 39: 70 type=188 (LJ14) 24 39 39: 71 type=189 (LJ14) 24 40 39: 72 type=190 (LJ14) 25 27 39: 73 type=190 (LJ14) 25 28 39: 74 type=190 (LJ14) 25 38 39: 75 type=191 (LJ14) 26 31 39: 76 type=191 (LJ14) 26 32 39: 77 type=191 (LJ14) 26 33 39: 78 type=191 (LJ14) 26 35 39: 79 type=191 (LJ14) 26 36 39: 80 type=191 (LJ14) 26 37 39: 81 type=190 (LJ14) 26 41 39: 82 type=192 (LJ14) 26 42 39: 83 type=193 (LJ14) 27 29 39: 84 type=191 (LJ14) 27 30 39: 85 type=191 (LJ14) 27 34 39: 86 type=194 (LJ14) 27 39 39: 87 type=186 (LJ14) 27 40 39: 88 type=195 (LJ14) 28 39 39: 89 type=187 (LJ14) 28 40 39: 90 type=193 (LJ14) 29 31 39: 91 type=193 (LJ14) 29 32 39: 92 type=193 (LJ14) 29 33 39: 93 type=193 (LJ14) 29 35 39: 94 type=193 (LJ14) 29 36 39: 95 type=193 (LJ14) 29 37 39: 96 type=196 (LJ14) 29 38 39: 97 type=191 (LJ14) 30 35 39: 98 type=191 (LJ14) 30 36 39: 99 type=191 (LJ14) 30 37 39: 100 type=197 (LJ14) 30 38 39: 101 type=191 (LJ14) 31 34 39: 102 type=191 (LJ14) 32 34 39: 103 type=191 (LJ14) 33 34 39: 104 type=197 (LJ14) 34 38 39: 105 type=196 (LJ14) 38 43 39: 106 type=197 (LJ14) 38 44 39: 107 type=198 (LJ14) 38 58 39: 108 type=190 (LJ14) 39 41 39: 109 type=195 (LJ14) 39 42 39: 110 type=186 (LJ14) 40 45 39: 111 type=186 (LJ14) 40 46 39: 112 type=199 (LJ14) 40 47 39: 113 type=188 (LJ14) 40 59 39: 114 type=189 (LJ14) 40 60 39: 115 type=190 (LJ14) 41 43 39: 116 type=190 (LJ14) 41 44 39: 117 type=190 (LJ14) 41 58 39: 118 type=200 (LJ14) 42 48 39: 119 type=200 (LJ14) 42 50 39: 120 type=190 (LJ14) 42 61 39: 121 type=192 (LJ14) 42 62 39: 122 type=193 (LJ14) 43 45 39: 123 type=193 (LJ14) 43 46 39: 124 type=201 (LJ14) 43 47 39: 125 type=194 (LJ14) 43 59 39: 126 type=186 (LJ14) 43 60 39: 127 type=202 (LJ14) 44 49 39: 128 type=202 (LJ14) 44 51 39: 129 type=200 (LJ14) 44 52 39: 130 type=200 (LJ14) 44 54 39: 131 type=195 (LJ14) 44 59 39: 132 type=187 (LJ14) 44 60 39: 133 type=201 (LJ14) 45 48 39: 134 type=201 (LJ14) 45 50 39: 135 type=196 (LJ14) 45 58 39: 136 type=201 (LJ14) 46 48 39: 137 type=201 (LJ14) 46 50 39: 138 type=196 (LJ14) 46 58 39: 139 type=203 (LJ14) 47 53 39: 140 type=203 (LJ14) 47 55 39: 141 type=204 (LJ14) 47 56 39: 142 type=205 (LJ14) 47 58 39: 143 type=203 (LJ14) 48 51 39: 144 type=204 (LJ14) 48 54 39: 145 type=203 (LJ14) 48 57 39: 146 type=203 (LJ14) 49 50 39: 147 type=206 (LJ14) 49 53 39: 148 type=203 (LJ14) 49 56 39: 149 type=204 (LJ14) 50 52 39: 150 type=203 (LJ14) 50 57 39: 151 type=206 (LJ14) 51 55 39: 152 type=203 (LJ14) 51 56 39: 153 type=203 (LJ14) 52 55 39: 154 type=203 (LJ14) 53 54 39: 155 type=206 (LJ14) 53 57 39: 156 type=206 (LJ14) 55 57 39: 157 type=196 (LJ14) 58 63 39: 158 type=196 (LJ14) 58 64 39: 159 type=198 (LJ14) 58 65 39: 160 type=190 (LJ14) 59 61 39: 161 type=195 (LJ14) 59 62 39: 162 type=188 (LJ14) 60 66 39: 163 type=189 (LJ14) 60 67 39: 164 type=190 (LJ14) 61 63 39: 165 type=190 (LJ14) 61 64 39: 166 type=190 (LJ14) 61 65 39: 167 type=190 (LJ14) 62 68 39: 168 type=192 (LJ14) 62 69 39: 169 type=194 (LJ14) 63 66 39: 170 type=186 (LJ14) 63 67 39: 171 type=194 (LJ14) 64 66 39: 172 type=186 (LJ14) 64 67 39: 173 type=196 (LJ14) 65 70 39: 174 type=197 (LJ14) 65 71 39: 175 type=198 (LJ14) 65 89 39: 176 type=190 (LJ14) 66 68 39: 177 type=195 (LJ14) 66 69 39: 178 type=186 (LJ14) 67 72 39: 179 type=186 (LJ14) 67 73 39: 180 type=187 (LJ14) 67 74 39: 181 type=188 (LJ14) 67 90 39: 182 type=189 (LJ14) 67 91 39: 183 type=190 (LJ14) 68 70 39: 184 type=190 (LJ14) 68 71 39: 185 type=190 (LJ14) 68 89 39: 186 type=191 (LJ14) 69 75 39: 187 type=191 (LJ14) 69 76 39: 188 type=192 (LJ14) 69 77 39: 189 type=190 (LJ14) 69 92 39: 190 type=192 (LJ14) 69 93 39: 191 type=193 (LJ14) 70 72 39: 192 type=193 (LJ14) 70 73 39: 193 type=191 (LJ14) 70 74 39: 194 type=194 (LJ14) 70 90 39: 195 type=186 (LJ14) 70 91 39: 196 type=191 (LJ14) 71 78 39: 197 type=191 (LJ14) 71 79 39: 198 type=187 (LJ14) 71 80 39: 199 type=195 (LJ14) 71 90 39: 200 type=187 (LJ14) 71 91 39: 201 type=193 (LJ14) 72 75 39: 202 type=193 (LJ14) 72 76 39: 203 type=191 (LJ14) 72 77 39: 204 type=196 (LJ14) 72 89 39: 205 type=193 (LJ14) 73 75 39: 206 type=193 (LJ14) 73 76 39: 207 type=191 (LJ14) 73 77 39: 208 type=196 (LJ14) 73 89 39: 209 type=190 (LJ14) 74 81 39: 210 type=207 (LJ14) 74 82 39: 211 type=197 (LJ14) 74 89 39: 212 type=193 (LJ14) 75 78 39: 213 type=193 (LJ14) 75 79 39: 214 type=186 (LJ14) 75 80 39: 215 type=193 (LJ14) 76 78 39: 216 type=193 (LJ14) 76 79 39: 217 type=186 (LJ14) 76 80 39: 218 type=187 (LJ14) 77 83 39: 219 type=187 (LJ14) 77 86 39: 220 type=190 (LJ14) 78 81 39: 221 type=208 (LJ14) 78 82 39: 222 type=190 (LJ14) 79 81 39: 223 type=208 (LJ14) 79 82 39: 224 type=190 (LJ14) 80 84 39: 225 type=190 (LJ14) 80 85 39: 226 type=190 (LJ14) 80 87 39: 227 type=190 (LJ14) 80 88 39: 228 type=190 (LJ14) 81 83 39: 229 type=190 (LJ14) 81 86 39: 230 type=190 (LJ14) 83 87 39: 231 type=190 (LJ14) 83 88 39: 232 type=190 (LJ14) 84 86 39: 233 type=190 (LJ14) 85 86 39: 234 type=196 (LJ14) 89 94 39: 235 type=197 (LJ14) 89 95 39: 236 type=198 (LJ14) 89 100 39: 237 type=190 (LJ14) 90 92 39: 238 type=195 (LJ14) 90 93 39: 239 type=186 (LJ14) 91 96 39: 240 type=186 (LJ14) 91 97 39: 241 type=209 (LJ14) 91 98 39: 242 type=188 (LJ14) 91 101 39: 243 type=189 (LJ14) 91 102 39: 244 type=190 (LJ14) 92 94 39: 245 type=190 (LJ14) 92 95 39: 246 type=190 (LJ14) 92 100 39: 247 type=190 (LJ14) 93 99 39: 248 type=190 (LJ14) 93 103 39: 249 type=192 (LJ14) 93 104 39: 250 type=193 (LJ14) 94 96 39: 251 type=193 (LJ14) 94 97 39: 252 type=210 (LJ14) 94 98 39: 253 type=194 (LJ14) 94 101 39: 254 type=186 (LJ14) 94 102 39: 255 type=195 (LJ14) 95 101 39: 256 type=187 (LJ14) 95 102 39: 257 type=190 (LJ14) 96 99 39: 258 type=196 (LJ14) 96 100 39: 259 type=190 (LJ14) 97 99 39: 260 type=196 (LJ14) 97 100 39: 261 type=211 (LJ14) 98 100 39: 262 type=196 (LJ14) 100 105 39: 263 type=197 (LJ14) 100 106 39: 264 type=198 (LJ14) 100 115 39: 265 type=190 (LJ14) 101 103 39: 266 type=195 (LJ14) 101 104 39: 267 type=186 (LJ14) 102 107 39: 268 type=186 (LJ14) 102 108 39: 269 type=187 (LJ14) 102 109 39: 270 type=188 (LJ14) 102 116 39: 271 type=189 (LJ14) 102 117 39: 272 type=190 (LJ14) 103 105 39: 273 type=190 (LJ14) 103 106 39: 274 type=190 (LJ14) 103 115 39: 275 type=191 (LJ14) 104 110 39: 276 type=191 (LJ14) 104 111 39: 277 type=197 (LJ14) 104 112 39: 278 type=190 (LJ14) 104 118 39: 279 type=192 (LJ14) 104 119 39: 280 type=193 (LJ14) 105 107 39: 281 type=193 (LJ14) 105 108 39: 282 type=191 (LJ14) 105 109 39: 283 type=194 (LJ14) 105 116 39: 284 type=186 (LJ14) 105 117 39: 285 type=195 (LJ14) 106 113 39: 286 type=195 (LJ14) 106 114 39: 287 type=195 (LJ14) 106 116 39: 288 type=187 (LJ14) 106 117 39: 289 type=193 (LJ14) 107 110 39: 290 type=193 (LJ14) 107 111 39: 291 type=196 (LJ14) 107 112 39: 292 type=196 (LJ14) 107 115 39: 293 type=193 (LJ14) 108 110 39: 294 type=193 (LJ14) 108 111 39: 295 type=196 (LJ14) 108 112 39: 296 type=196 (LJ14) 108 115 39: 297 type=197 (LJ14) 109 115 39: 298 type=194 (LJ14) 110 113 39: 299 type=194 (LJ14) 110 114 39: 300 type=194 (LJ14) 111 113 39: 301 type=194 (LJ14) 111 114 39: 302 type=196 (LJ14) 115 120 39: 303 type=197 (LJ14) 115 121 39: 304 type=198 (LJ14) 115 134 39: 305 type=190 (LJ14) 116 118 39: 306 type=195 (LJ14) 116 119 39: 307 type=186 (LJ14) 117 122 39: 308 type=186 (LJ14) 117 123 39: 309 type=187 (LJ14) 117 124 39: 310 type=188 (LJ14) 117 135 39: 311 type=189 (LJ14) 117 136 39: 312 type=190 (LJ14) 118 120 39: 313 type=190 (LJ14) 118 121 39: 314 type=190 (LJ14) 118 134 39: 315 type=191 (LJ14) 119 125 39: 316 type=192 (LJ14) 119 126 39: 317 type=192 (LJ14) 119 130 39: 318 type=190 (LJ14) 119 137 39: 319 type=192 (LJ14) 119 138 39: 320 type=193 (LJ14) 120 122 39: 321 type=193 (LJ14) 120 123 39: 322 type=191 (LJ14) 120 124 39: 323 type=194 (LJ14) 120 135 39: 324 type=186 (LJ14) 120 136 39: 325 type=191 (LJ14) 121 127 39: 326 type=191 (LJ14) 121 128 39: 327 type=191 (LJ14) 121 129 39: 328 type=191 (LJ14) 121 131 39: 329 type=191 (LJ14) 121 132 39: 330 type=191 (LJ14) 121 133 39: 331 type=195 (LJ14) 121 135 39: 332 type=187 (LJ14) 121 136 39: 333 type=193 (LJ14) 122 125 39: 334 type=191 (LJ14) 122 126 39: 335 type=191 (LJ14) 122 130 39: 336 type=196 (LJ14) 122 134 39: 337 type=193 (LJ14) 123 125 39: 338 type=191 (LJ14) 123 126 39: 339 type=191 (LJ14) 123 130 39: 340 type=196 (LJ14) 123 134 39: 341 type=197 (LJ14) 124 134 39: 342 type=193 (LJ14) 125 127 39: 343 type=193 (LJ14) 125 128 39: 344 type=193 (LJ14) 125 129 39: 345 type=193 (LJ14) 125 131 39: 346 type=193 (LJ14) 125 132 39: 347 type=193 (LJ14) 125 133 39: 348 type=191 (LJ14) 126 131 39: 349 type=191 (LJ14) 126 132 39: 350 type=191 (LJ14) 126 133 39: 351 type=191 (LJ14) 127 130 39: 352 type=191 (LJ14) 128 130 39: 353 type=191 (LJ14) 129 130 39: 354 type=196 (LJ14) 134 139 39: 355 type=197 (LJ14) 134 140 39: 356 type=198 (LJ14) 134 144 39: 357 type=190 (LJ14) 135 137 39: 358 type=195 (LJ14) 135 138 39: 359 type=186 (LJ14) 136 141 39: 360 type=186 (LJ14) 136 142 39: 361 type=186 (LJ14) 136 143 39: 362 type=188 (LJ14) 136 145 39: 363 type=189 (LJ14) 136 146 39: 364 type=190 (LJ14) 137 139 39: 365 type=190 (LJ14) 137 140 39: 366 type=190 (LJ14) 137 144 39: 367 type=190 (LJ14) 138 147 39: 368 type=192 (LJ14) 138 148 39: 369 type=193 (LJ14) 139 141 39: 370 type=193 (LJ14) 139 142 39: 371 type=193 (LJ14) 139 143 39: 372 type=194 (LJ14) 139 145 39: 373 type=186 (LJ14) 139 146 39: 374 type=195 (LJ14) 140 145 39: 375 type=187 (LJ14) 140 146 39: 376 type=196 (LJ14) 141 144 39: 377 type=196 (LJ14) 142 144 39: 378 type=196 (LJ14) 143 144 39: 379 type=196 (LJ14) 144 149 39: 380 type=197 (LJ14) 144 150 39: 381 type=198 (LJ14) 144 154 39: 382 type=190 (LJ14) 145 147 39: 383 type=195 (LJ14) 145 148 39: 384 type=186 (LJ14) 146 151 39: 385 type=186 (LJ14) 146 152 39: 386 type=186 (LJ14) 146 153 39: 387 type=188 (LJ14) 146 155 39: 388 type=190 (LJ14) 147 149 39: 389 type=190 (LJ14) 147 150 39: 390 type=190 (LJ14) 147 154 39: 391 type=193 (LJ14) 149 151 39: 392 type=193 (LJ14) 149 152 39: 393 type=193 (LJ14) 149 153 39: 394 type=194 (LJ14) 149 155 39: 395 type=195 (LJ14) 150 155 39: 396 type=196 (LJ14) 151 154 39: 397 type=196 (LJ14) 152 154 39: 398 type=196 (LJ14) 153 154 39: Coulomb-14: 39: nr: 0 39: LJC-14 q: 39: nr: 0 39: LJC Pairs NB: 39: nr: 0 39: LJ (SR): 39: nr: 0 39: Buck.ham (SR): 39: nr: 0 39: LJ (unused): 39: nr: 0 39: B.ham (unused): 39: nr: 0 39: Disper. corr.: 39: nr: 0 39: Coulomb (SR): 39: nr: 0 39: Coul (unused): 39: nr: 0 39: RF excl.: 39: nr: 0 39: Coul. recip.: 39: nr: 0 39: LJ recip.: 39: nr: 0 39: DPD: 39: nr: 0 39: Polarization: 39: nr: 0 39: Water Pol.: 39: nr: 0 39: Thole Pol.: 39: nr: 0 39: Anharm. Pol.: 39: nr: 0 39: Position Rest.: 39: nr: 0 39: Flat-bottom posres: 39: nr: 0 39: Dis. Rest.: 39: nr: 0 39: D.R.Viol. (nm): 39: nr: 0 39: Orient. Rest.: 39: nr: 0 39: Ori. R. RMSD: 39: nr: 0 39: Angle Rest.: 39: nr: 0 39: Angle Rest. Z: 39: nr: 0 39: Dih. Rest.: 39: nr: 0 39: Dih. Rest. Viol.: 39: nr: 0 39: Constraint: 39: nr: 0 39: Constr. No Conn.: 39: nr: 0 39: Settle: 39: nr: 0 39: Virtual site 2: 39: nr: 0 39: Virtual site 2fd: 39: nr: 0 39: Virtual site 3: 39: nr: 0 39: Virtual site 3fd: 39: nr: 0 39: Virtual site 3fad: 39: nr: 0 39: Virtual site 3out: 39: nr: 0 39: Virtual site 4fd: 39: nr: 0 39: Virtual site 4fdn: 39: nr: 0 39: Virtual site N: 39: nr: 0 39: COM Pull En.: 39: nr: 0 39: Density fitting: 39: nr: 0 39: Quantum En.: 39: nr: 0 39: Potential: 39: nr: 0 39: Kinetic En.: 39: nr: 0 39: Total Energy: 39: nr: 0 39: Conserved En.: 39: nr: 0 39: Temperature: 39: nr: 0 39: Vir. Temp. (not used): 39: nr: 0 39: Pres. DC: 39: nr: 0 39: Pressure: 39: nr: 0 39: dH/dl constr.: 39: nr: 0 39: dVremain/dl: 39: nr: 0 39: dEkin/dl: 39: nr: 0 39: dVcoul/dl: 39: nr: 0 39: dVvdw/dl: 39: nr: 0 39: dVbonded/dl: 39: nr: 0 39: dVrestraint/dl: 39: nr: 0 39: dVtemperature/dl: 39: nr: 0 39: grp[T-Coupling ] nr=1, name=[ rest] 39: grp[Energy Mon. ] nr=1, name=[ rest] 39: grp[Acceleration] nr=1, name=[ rest] 39: grp[Freeze ] nr=1, name=[ rest] 39: grp[User1 ] nr=1, name=[ rest] 39: grp[User2 ] nr=1, name=[ rest] 39: grp[VCM ] nr=1, name=[ rest] 39: grp[Compressed X] nr=1, name=[ rest] 39: grp[Or. Res. Fit] nr=1, name=[ rest] 39: grp[QMMM ] nr=1, name=[ rest] 39: grpname (11): 39: grpname[0]={name="System"} 39: grpname[1]={name="Protein"} 39: grpname[2]={name="Protein-H"} 39: grpname[3]={name="C-alpha"} 39: grpname[4]={name="Backbone"} 39: grpname[5]={name="MainChain"} 39: grpname[6]={name="MainChain+Cb"} 39: grpname[7]={name="MainChain+H"} 39: grpname[8]={name="SideChain"} 39: grpname[9]={name="SideChain-H"} 39: grpname[10]={name="rest"} 39: groups T-Cou Energ Accel Freez User1 User2 VCM Compr Or. R QMMM 39: allocated 0 0 0 0 0 0 0 0 0 0 39: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0 39: box (3x3): 39: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00} 39: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00} 39: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00} 39: box_rel (3x3): 39: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: boxv (3x3): 39: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: pres_prev (3x3): 39: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: svir_prev (3x3): 39: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: fvir_prev (3x3): 39: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: nosehoover_xi: not available 39: x (156x3): 39: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00} 39: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00} 39: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00} 39: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00} 39: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00} 39: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00} 39: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00} 39: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00} 39: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01} 39: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01} 39: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01} 39: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00} 39: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01} 39: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01} 39: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01} 39: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01} 39: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01} 39: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01} 39: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01} 39: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01} 39: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01} 39: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01} 39: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00} 39: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00} 39: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00} 39: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00} 39: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00} 39: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01} 39: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00} 39: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00} 39: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00} 39: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00} 39: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01} 39: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01} 39: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00} 39: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00} 39: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00} 39: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00} 39: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01} 39: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01} 39: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01} 39: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01} 39: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01} 39: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01} 39: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01} 39: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01} 39: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01} 39: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01} 39: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01} 39: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01} 39: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01} 39: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01} 39: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01} 39: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01} 39: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01} 39: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01} 39: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01} 39: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01} 39: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01} 39: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01} 39: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01} 39: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01} 39: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01} 39: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01} 39: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01} 39: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01} 39: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01} 39: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01} 39: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01} 39: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01} 39: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01} 39: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01} 39: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01} 39: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01} 39: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02} 39: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02} 39: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02} 39: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02} 39: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02} 39: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01} 39: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02} 39: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01} 39: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02} 39: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01} 39: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01} 39: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01} 39: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02} 39: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01} 39: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02} 39: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01} 39: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02} 39: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01} 39: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01} 39: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02} 39: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02} 39: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02} 39: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01} 39: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02} 39: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02} 39: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02} 39: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02} 39: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02} 39: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01} 39: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01} 39: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01} 39: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01} 39: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01} 39: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01} 39: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01} 39: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01} 39: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01} 39: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01} 39: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01} 39: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01} 39: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01} 39: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01} 39: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01} 39: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01} 39: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01} 39: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01} 39: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01} 39: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01} 39: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01} 39: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01} 39: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01} 39: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02} 39: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01} 39: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01} 39: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01} 39: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01} 39: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01} 39: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01} 39: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01} 39: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01} 39: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02} 39: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02} 39: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02} 39: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02} 39: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01} 39: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01} 39: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01} 39: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01} 39: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01} 39: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01} 39: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01} 39: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01} 39: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01} 39: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01} 39: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01} 39: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01} 39: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01} 39: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01} 39: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01} 39: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02} 39: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01} 39: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01} 39: v (156x3): 39: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: Group statistics 39: T-Coupling : 156 (total 156 atoms) 39: Energy Mon. : 156 (total 156 atoms) 39: Acceleration: 156 (total 156 atoms) 39: Freeze : 156 (total 156 atoms) 39: User1 : 156 (total 156 atoms) 39: User2 : 156 (total 156 atoms) 39: VCM : 156 (total 156 atoms) 39: Compressed X: 156 (total 156 atoms) 39: Or. Res. Fit: 156 (total 156 atoms) 39: QMMM : 156 (total 156 atoms) 39: [ OK ] DumpTest.WorksWithTpr (11 ms) 39: [ RUN ] DumpTest.WorksWithTprAndMdpWriting 39: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 39: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 39: [ OK ] DumpTest.WorksWithTprAndMdpWriting (2 ms) 39: [----------] 2 tests from DumpTest (13 ms total) 39: 39: [----------] 4 tests from ReportMethodsTest 39: 39: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 39: For a correct single-point energy evaluation with nsteps = 0, use 39: continuation = yes to avoid constraining the input coordinates. 39: 39: Setting the LD random seed to -1179656402 39: Generated 330891 of the 330891 non-bonded parameter combinations 39: Generating 1-4 interactions: fudge = 0.5 39: Generated 330891 of the 330891 1-4 parameter combinations 39: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 39: 39: NOTE 2 [file lysozyme.top, line 1465]: 39: System has non-zero total charge: 2.000000 39: Total charge should normally be an integer. See 39: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 39: for discussion on how close it should be to an integer. 39: 39: 39: 39: Number of degrees of freedom in T-Coupling group rest is 465.00 39: 39: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 39: NVE simulation with an initial temperature of zero: will use a Verlet 39: buffer of 10%. Check your energy drift! 39: 39: 39: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 39: You are using a plain Coulomb cut-off, which might produce artifacts. 39: You might want to consider using PME electrostatics. 39: 39: 39: 39: There were 4 notes 39: Analysing residue names: 39: There are: 10 Protein residues 39: Analysing Protein... 39: This run will generate roughly 0 Mb of data 39: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated 39: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) 39: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted 39: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) 39: [ RUN ] ReportMethodsTest.WritesCorrectInformation 39: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 39: [ OK ] ReportMethodsTest.WritesCorrectInformation (1 ms) 39: [ RUN ] ReportMethodsTest.ToolEndToEndTest 39: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 39: section: Methods 39: subsection: Simulation system 39: A system of 1 molecules (156 atoms) was simulated. 39: 39: subsection: Simulation settings 39: A total of 0 ns were simulated with a time step of 1 fs. 39: Neighbor searching was performed every 10 steps. 39: The Cut-off algorithm was used for electrostatic interactions. 39: with a cut-off of 1 nm. 39: A single cut-off of 1.1 nm was used for Van der Waals interactions. 39: [ OK ] ReportMethodsTest.ToolEndToEndTest (1 ms) 39: [----------] 4 tests from ReportMethodsTest (2 ms total) 39: 39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0 39: Will write tng: Trajectory file (tng format) 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: trr version: GMX_trn_file (single precision) 39: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0 (30 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1 39: Will write tng: Trajectory file (tng format) 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frame 0 time 0.000 39: Precision of /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 39: -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1 (7 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2 39: Will write tng: Trajectory file (tng format) 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2 (6 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3 39: Will write tng: Trajectory file (tng format) 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frames from gro file '', 6 atoms. 39: Reading frame 0 time 0.000 39: Precision of /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 39: -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3 (5 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4 39: Will write tng: Trajectory file (tng format) 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 39: Precision of /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 39: -> frame 0 time 0.000 't= 0.00000', 6 atoms 39: Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4 (6 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5 39: Will write tng: Trajectory file (tng format) 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5 (4 ms) 39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset (58 ms total) 39: 39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0 39: Will write trr: Trajectory in portable xdr format 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0 (2 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1 39: Will write trr: Trajectory in portable xdr format 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frame 0 time 0.000 39: Precision of /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 39: -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1 (2 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2 39: Will write trr: Trajectory in portable xdr format 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2 (1 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3 39: Will write trr: Trajectory in portable xdr format 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frames from gro file '', 6 atoms. 39: Reading frame 0 time 0.000 39: Precision of /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 39: -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3 (2 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4 39: Will write trr: Trajectory in portable xdr format 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 39: Precision of /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 39: -> frame 0 time 0.000 't= 0.00000', 6 atoms 39: Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4 (1 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5 39: Will write trr: Trajectory in portable xdr format 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5 (2 ms) 39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile (10 ms total) 39: 39: [----------] Global test environment tear-down 39: [==========] 18 tests from 4 test cases ran. (1425 ms total) 39: [ PASSED ] 18 tests. 39/54 Test #39: ToolUnitTests ....................... Passed 1.44 sec test 40 Start 40: FileIOTests 40: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/fileio-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/FileIOTests.xml" 40: Test timeout computed to be: 30 40: [==========] Running 33 tests from 8 test cases. 40: [----------] Global test environment set-up. 40: [----------] 2 tests from FileMD5Test 40: [ RUN ] FileMD5Test.CanComputeMD5 40: [ OK ] FileMD5Test.CanComputeMD5 (1 ms) 40: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 40: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (1 ms) 40: [----------] 2 tests from FileMD5Test (2 ms total) 40: 40: [----------] 3 tests from MrcSerializer 40: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet 40: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) 40: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize 40: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms) 40: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip 40: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (1 ms) 40: [----------] 3 tests from MrcSerializer (1 ms total) 40: 40: [----------] 4 tests from MrcDensityMap 40: [ RUN ] MrcDensityMap.RoundTripIsIdempotent 40: [ OK ] MrcDensityMap.RoundTripIsIdempotent (30 ms) 40: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent 40: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms) 40: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile 40: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms) 40: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile 40: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (3 ms) 40: [----------] 4 tests from MrcDensityMap (34 ms total) 40: 40: [----------] 8 tests from MrcDensityMapHeaderTest 40: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader 40: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) 40: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect 40: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) 40: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid 40: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms) 40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven 40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) 40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined 40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms) 40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues 40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) 40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents 40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) 40: [ RUN ] MrcDensityMapHeaderTest.IsSane 40: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) 40: [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total) 40: 40: [----------] 9 tests from ReadTest 40: [ RUN ] ReadTest.get_eint_ReadsInteger 40: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 40: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 40: 40: ERROR 1 [file unknown, line 0]: 40: Right hand side '0.8' for parameter 'test' in parameter file is not an 40: integer value 40: 40: 40: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 40: [ RUN ] ReadTest.get_eint_WarnsAboutString 40: 40: ERROR 1 [file unknown, line 0]: 40: Right hand side 'hello' for parameter 'test' in parameter file is not an 40: integer value 40: 40: 40: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 40: [ RUN ] ReadTest.get_eint64_ReadsInteger 40: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 40: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 40: 40: ERROR 1 [file unknown, line 0]: 40: Right hand side '0.8' for parameter 'test' in parameter file is not an 40: integer value 40: 40: 40: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 40: [ RUN ] ReadTest.get_eint64_WarnsAboutString 40: 40: ERROR 1 [file unknown, line 0]: 40: Right hand side 'hello' for parameter 'test' in parameter file is not an 40: integer value 40: 40: 40: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 40: [ RUN ] ReadTest.get_ereal_ReadsInteger 40: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 40: [ RUN ] ReadTest.get_ereal_ReadsFloat 40: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 40: [ RUN ] ReadTest.get_ereal_WarnsAboutString 40: 40: ERROR 1 [file unknown, line 0]: 40: Right hand side 'hello' for parameter 'test' in parameter file is not a 40: real value 40: 40: 40: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 40: [----------] 9 tests from ReadTest (0 ms total) 40: 40: [----------] 1 test from FileIOXdrSerializerTest 40: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect 40: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (1 ms) 40: [----------] 1 test from FileIOXdrSerializerTest (1 ms total) 40: 40: [----------] 2 tests from TngTest 40: [ RUN ] TngTest.CanOpenTngFile 40: TNG library: Cannot open file spc2-traj.tng. ./src/external/tng_io/src/lib/tng_io.c: 890 40: TNG library: Cannot open file spc2-traj.tng. ./src/external/tng_io/src/lib/tng_io.c: 890 40: [ OK ] TngTest.CanOpenTngFile (0 ms) 40: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 40: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 40: [----------] 2 tests from TngTest (0 ms total) 40: 40: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (1 ms) 40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (1 ms) 40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (2 ms) 40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (1 ms) 40: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (5 ms total) 40: 40: [----------] Global test environment tear-down 40: [==========] 33 tests from 8 test cases ran. (43 ms total) 40: [ PASSED ] 33 tests. 40/54 Test #40: FileIOTests ......................... Passed 0.06 sec test 41 Start 41: SelectionUnitTests 41: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/selection-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/SelectionUnitTests.xml" 41: Test timeout computed to be: 30 41: [==========] Running 192 tests from 11 test cases. 41: [----------] Global test environment set-up. 41: [----------] 1 test from IndexGroupTest 41: [ RUN ] IndexGroupTest.RemovesDuplicates 41: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 41: [----------] 1 test from IndexGroupTest (0 ms total) 41: 41: [----------] 15 tests from IndexBlockTest 41: [ RUN ] IndexBlockTest.CreatesUnknownBlock 41: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms) 41: [ RUN ] IndexBlockTest.CreatesAtomBlock 41: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms) 41: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology 41: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (1 ms) 41: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology 41: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (0 ms) 41: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology 41: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms) 41: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology 41: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (1 ms) 41: [ RUN ] IndexBlockTest.CreatesSingleBlock 41: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) 41: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 41: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) 41: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 41: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) 41: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 41: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 41: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) 41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 41: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 41: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 41: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 41: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 41: [----------] 15 tests from IndexBlockTest (2 ms total) 41: 41: [----------] 11 tests from IndexMapTest 41: [ RUN ] IndexMapTest.InitializesAtomBlock 41: [ OK ] IndexMapTest.InitializesAtomBlock (1 ms) 41: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 41: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms) 41: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 41: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms) 41: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 41: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) 41: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 41: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms) 41: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 41: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (1 ms) 41: [ RUN ] IndexMapTest.InitializesMoleculeBlock 41: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms) 41: [ RUN ] IndexMapTest.MapsSingleBlock 41: [ OK ] IndexMapTest.MapsSingleBlock (0 ms) 41: [ RUN ] IndexMapTest.MapsResidueBlocks 41: [ OK ] IndexMapTest.MapsResidueBlocks (0 ms) 41: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 41: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (1 ms) 41: [ RUN ] IndexMapTest.HandlesMultipleRequests 41: [ OK ] IndexMapTest.HandlesMultipleRequests (1 ms) 41: [----------] 11 tests from IndexMapTest (4 ms total) 41: 41: [----------] 3 tests from IndexGroupsAndNamesTest 41: [ RUN ] IndexGroupsAndNamesTest.containsNames 41: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms) 41: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing 41: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms) 41: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect 41: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms) 41: [----------] 3 tests from IndexGroupsAndNamesTest (0 ms total) 41: 41: [----------] 15 tests from NeighborhoodSearchTest 41: [ RUN ] NeighborhoodSearchTest.SimpleSearch 41: [ OK ] NeighborhoodSearchTest.SimpleSearch (19 ms) 41: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 41: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (20 ms) 41: [ RUN ] NeighborhoodSearchTest.GridSearchBox 41: [ OK ] NeighborhoodSearchTest.GridSearchBox (30 ms) 41: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 41: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (9 ms) 41: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 41: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (5 ms) 41: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 41: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (2 ms) 41: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 41: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (3 ms) 41: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 41: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 41: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 41: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (31 ms) 41: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 41: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (1 ms) 41: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 41: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 41: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 41: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 41: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 41: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 41: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 41: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (4 ms) 41: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 41: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (0 ms) 41: [----------] 15 tests from NeighborhoodSearchTest (124 ms total) 41: 41: [----------] 12 tests from PositionCalculationTest 41: [ RUN ] PositionCalculationTest.ComputesAtomPositions 41: [ OK ] PositionCalculationTest.ComputesAtomPositions (1 ms) 41: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 41: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms) 41: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 41: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (0 ms) 41: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 41: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms) 41: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 41: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms) 41: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 41: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (1 ms) 41: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 41: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms) 41: [ RUN ] PositionCalculationTest.ComputesPositionMask 41: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms) 41: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 41: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms) 41: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 41: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (1 ms) 41: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 41: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (0 ms) 41: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 41: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (0 ms) 41: [----------] 12 tests from PositionCalculationTest (3 ms total) 41: 41: [----------] 29 tests from SelectionCollectionTest 41: [ RUN ] SelectionCollectionTest.HandlesNoSelections 41: [ OK ] SelectionCollectionTest.HandlesNoSelections (1 ms) 41: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 41: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 41: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 41: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (0 ms) 41: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 41: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 41: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 41: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 41: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 41: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 41: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (1 ms) 41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 41: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 41: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 41: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 41: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 41: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (0 ms) 41: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 41: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (0 ms) 41: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 41: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (1 ms) 41: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 41: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (0 ms) 41: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 41: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (0 ms) 41: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 41: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (0 ms) 41: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 41: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (1 ms) 41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (1 ms) 41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (0 ms) 41: [----------] 29 tests from SelectionCollectionTest (8 ms total) 41: 41: [----------] 14 tests from SelectionCollectionInteractiveTest 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 41: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (0 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 41: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (1 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 41: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (0 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 41: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (0 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 41: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (1 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 41: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (0 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 41: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (0 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 41: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (0 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 41: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (0 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 41: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (0 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 41: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (1 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 41: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (0 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 41: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (0 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 41: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (1 ms) 41: [----------] 14 tests from SelectionCollectionInteractiveTest (5 ms total) 41: 41: [----------] 66 tests from SelectionCollectionDataTest 41: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 41: [ OK ] SelectionCollectionDataTest.HandlesAllNone (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 41: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesResnr 41: [ OK ] SelectionCollectionDataTest.HandlesResnr (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 41: [ OK ] SelectionCollectionDataTest.HandlesResIndex (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 41: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 41: [ OK ] SelectionCollectionDataTest.HandlesAtomname (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 41: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 41: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesChain 41: [ OK ] SelectionCollectionDataTest.HandlesChain (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesMass 41: [ OK ] SelectionCollectionDataTest.HandlesMass (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesCharge 41: [ OK ] SelectionCollectionDataTest.HandlesCharge (21 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 41: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 41: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 41: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesBeta 41: [ OK ] SelectionCollectionDataTest.HandlesBeta (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesResname 41: [ OK ] SelectionCollectionDataTest.HandlesResname (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 41: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 41: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 41: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 41: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (2 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 41: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 41: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 41: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 41: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (5 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 41: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (2 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 41: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (2 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 41: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (1 ms) 41: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 41: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (1 ms) 41: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 41: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 41: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 41: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 41: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 41: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 41: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 41: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 41: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 41: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 41: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 41: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 41: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 41: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 41: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 41: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 41: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 41: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 41: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 41: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 41: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 41: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 41: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 41: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 41: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 41: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 41: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 41: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 41: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 41: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 41: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 41: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 41: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 41: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 41: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 41: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 41: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 41: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 41: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (1 ms) 41: [----------] 66 tests from SelectionCollectionDataTest (72 ms total) 41: 41: [----------] 17 tests from SelectionOptionTest 41: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 41: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 41: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 41: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (1 ms) 41: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 41: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (0 ms) 41: [ RUN ] SelectionOptionTest.ChecksEmptySelections 41: [ OK ] SelectionOptionTest.ChecksEmptySelections (0 ms) 41: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 41: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesTooManySelections 41: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 41: [ OK ] SelectionOptionTest.HandlesTooFewSelections (1 ms) 41: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 41: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesAdjuster 41: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 41: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 41: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 41: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (1 ms) 41: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 41: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 41: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 41: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 41: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms) 41: [----------] 17 tests from SelectionOptionTest (3 ms total) 41: 41: [----------] 9 tests from SelectionFileOptionTest 41: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 41: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (0 ms) 41: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 41: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (1 ms) 41: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 41: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) 41: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 41: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (0 ms) 41: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 41: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (1 ms) 41: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 41: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (0 ms) 41: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 41: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms) 41: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 41: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (1 ms) 41: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 41: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (0 ms) 41: [----------] 9 tests from SelectionFileOptionTest (3 ms total) 41: 41: [----------] Global test environment tear-down 41: [==========] 192 tests from 11 test cases ran. (224 ms total) 41: [ PASSED ] 192 tests. 41/54 Test #41: SelectionUnitTests .................. Passed 0.24 sec test 42 Start 42: MdrunOutputTests 42: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/MdrunOutputTests.xml" 42: Test timeout computed to be: 600 42: [==========] Running 12 tests from 5 test cases. 42: [----------] Global test environment set-up. 42: [----------] 1 test from MdrunTest 42: [ RUN ] MdrunTest.WritesHelp 42: [ OK ] MdrunTest.WritesHelp (2 ms) 42: [----------] 1 test from MdrunTest (2 ms total) 42: 42: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput 42: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 42: Setting the LD random seed to -884785 42: Generated 3 of the 3 non-bonded parameter combinations 42: Generating 1-4 interactions: fudge = 0.5 42: Generated 3 of the 3 1-4 parameter combinations 42: Excluding 2 bonded neighbours molecule type 'SOL' 42: Number of degrees of freedom in T-Coupling group rest is 9.00 42: 42: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 42: NVE simulation: will use the initial temperature of 2573.591 K for 42: determining the Verlet buffer size 42: 42: 42: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 42: You are using a plain Coulomb cut-off, which might produce artifacts. 42: You might want to consider using PME electrostatics. 42: 42: 42: 42: There were 2 notes 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 42: Can not increase nstlist because an NVE ensemble is used 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'spc2' 42: 1 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 42: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm 42: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.017 0.009 198.2 42: (ns/day) (hour/ns) 42: Performance: 20.229 1.186 42: Reading frame 0 time 0.000 42: # Atoms 6 42: Reading frame 1 time 0.001 Last frame 1 time 0.001 42: 42: 42: Item #frames Timestep (ps) 42: Step 2 0.001 42: Time 2 0.001 42: Lambda 0 42: Coords 2 0.001 42: Velocities 0 42: Forces 0 42: Box 2 0.001 42: Checking file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc 42: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (142 ms) 42: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 42: Setting the LD random seed to -310650945 42: Generated 3 of the 3 non-bonded parameter combinations 42: Generating 1-4 interactions: fudge = 0.5 42: Generated 3 of the 3 1-4 parameter combinations 42: Excluding 2 bonded neighbours molecule type 'SOL' 42: Number of degrees of freedom in T-Coupling group rest is 9.00 42: 42: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 42: NVE simulation: will use the initial temperature of 2573.591 K for 42: determining the Verlet buffer size 42: 42: 42: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 42: You are using a plain Coulomb cut-off, which might produce artifacts. 42: You might want to consider using PME electrostatics. 42: 42: 42: 42: There were 2 notes 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 42: Can not increase nstlist because an NVE ensemble is used 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'spc2' 42: 1 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 42: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm 42: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.005 0.003 194.8 42: (ns/day) (hour/ns) 42: Performance: 62.697 0.383 42: Reading frame 0 time 0.000 42: # Atoms 6 42: Reading frame 1 time 0.001 Last frame 1 time 0.001 42: 42: 42: Item #frames Timestep (ps) 42: Step 2 0.001 42: Time 2 0.001 42: Lambda 0 42: Coords 2 0.001 42: Velocities 0 42: Forces 0 42: Box 2 0.001 42: Checking file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc 42: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (11 ms) 42: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 42: Setting the LD random seed to -279445537 42: Generated 3 of the 3 non-bonded parameter combinations 42: Generating 1-4 interactions: fudge = 0.5 42: Generated 3 of the 3 1-4 parameter combinations 42: Excluding 2 bonded neighbours molecule type 'SOL' 42: Number of degrees of freedom in T-Coupling group rest is 9.00 42: 42: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 42: NVE simulation: will use the initial temperature of 2573.591 K for 42: determining the Verlet buffer size 42: 42: 42: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 42: You are using a plain Coulomb cut-off, which might produce artifacts. 42: You might want to consider using PME electrostatics. 42: 42: 42: 42: There were 2 notes 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 42: Can not increase nstlist because an NVE ensemble is used 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'spc2' 42: 1 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 42: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm 42: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.005 0.003 195.0 42: (ns/day) (hour/ns) 42: Performance: 64.991 0.369 42: Reading frame 0 time 0.000 42: # Atoms 3 42: Reading frame 1 time 0.001 Last frame 1 time 0.001 42: 42: 42: Item #frames Timestep (ps) 42: Step 2 0.001 42: Time 2 0.001 42: Lambda 0 42: Coords 2 0.001 42: Velocities 0 42: Forces 0 42: Box 2 0.001 42: Checking file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc 42: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (10 ms) 42: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (163 ms total) 42: 42: [----------] 2 tests from Argon12/OutputFiles 42: [ RUN ] Argon12/OutputFiles.FilesArePresent/0 42: 42: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 42: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 42: that with the Verlet scheme, nstlist has no effect on the accuracy of 42: your simulation. 42: 42: 42: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 42: Setting nstcalcenergy (100) equal to nstenergy (4) 42: 42: Generated 1 of the 1 non-bonded parameter combinations 42: Excluding 1 bonded neighbours molecule type 'Argon' 42: Number of degrees of freedom in T-Coupling group System is 33.00 42: 42: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 42: NVE simulation: will use the initial temperature of 68.810 K for 42: determining the Verlet buffer size 42: 42: 42: There were 3 notes 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 42: Can not increase nstlist because an NVE ensemble is used 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'Argon' 42: 16 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 42: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 42: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.006 0.003 195.3 42: (ns/day) (hour/ns) 42: Performance: 487.389 0.049 42: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (10 ms) 42: [ RUN ] Argon12/OutputFiles.FilesArePresent/1 42: 42: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 42: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 42: that with the Verlet scheme, nstlist has no effect on the accuracy of 42: your simulation. 42: 42: 42: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 42: Setting nstcalcenergy (100) equal to nstenergy (4) 42: 42: Generated 1 of the 1 non-bonded parameter combinations 42: Excluding 1 bonded neighbours molecule type 'Argon' 42: Number of degrees of freedom in T-Coupling group System is 33.00 42: 42: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 42: NVE simulation: will use the initial temperature of 68.810 K for 42: determining the Verlet buffer size 42: 42: 42: There were 3 notes 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 42: Can not increase nstlist because an NVE ensemble is used 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'Argon' 42: 16 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 42: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 42: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.012 0.006 198.2 42: (ns/day) (hour/ns) 42: Performance: 234.484 0.102 42: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (13 ms) 42: [----------] 2 tests from Argon12/OutputFiles (23 ms total) 42: 42: [----------] 3 tests from MdrunCanWrite/Trajectories 42: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 42: Setting the LD random seed to -948063265 42: Generated 8 of the 10 non-bonded parameter combinations 42: Excluding 2 bonded neighbours molecule type 'Methanol' 42: Excluding 2 bonded neighbours molecule type 'SOL' 42: Number of degrees of freedom in T-Coupling group System is 12.00 42: 42: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: 42: You are using a plain Coulomb cut-off, which might produce artifacts. 42: You might want to consider using PME electrostatics. 42: 42: 42: 42: There was 1 note 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 42: 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'spc-and-methanol' 42: 6 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.015 0.008 197.5 42: (ns/day) (hour/ns) 42: Performance: 79.151 0.303 42: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (60 ms) 42: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 42: Setting the LD random seed to -35162369 42: Generated 8 of the 10 non-bonded parameter combinations 42: Excluding 2 bonded neighbours molecule type 'Methanol' 42: Excluding 2 bonded neighbours molecule type 'SOL' 42: Number of degrees of freedom in T-Coupling group System is 12.00 42: 42: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: 42: You are using a plain Coulomb cut-off, which might produce artifacts. 42: You might want to consider using PME electrostatics. 42: 42: 42: 42: There was 1 note 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 42: 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'spc-and-methanol' 42: 6 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.015 0.008 198.2 42: (ns/day) (hour/ns) 42: Performance: 79.606 0.301 42: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (19 ms) 42: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 42: Setting the LD random seed to -340787206 42: Generated 8 of the 10 non-bonded parameter combinations 42: Excluding 2 bonded neighbours molecule type 'Methanol' 42: Excluding 2 bonded neighbours molecule type 'SOL' 42: Number of degrees of freedom in T-Coupling group System is 12.00 42: 42: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: 42: You are using a plain Coulomb cut-off, which might produce artifacts. 42: You might want to consider using PME electrostatics. 42: 42: 42: 42: There was 1 note 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 42: 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'spc-and-methanol' 42: 6 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.008 0.004 197.1 42: (ns/day) (hour/ns) 42: Performance: 152.465 0.157 42: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (10 ms) 42: [----------] 3 tests from MdrunCanWrite/Trajectories (90 ms total) 42: 42: [----------] 3 tests from MdrunCanWrite/NptTrajectories 42: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 42: Setting the LD random seed to -34670721 42: Generated 8 of the 10 non-bonded parameter combinations 42: Excluding 2 bonded neighbours molecule type 'Methanol' 42: Excluding 2 bonded neighbours molecule type 'SOL' 42: Number of degrees of freedom in T-Coupling group System is 12.00 42: 42: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: 42: You are using a plain Coulomb cut-off, which might produce artifacts. 42: You might want to consider using PME electrostatics. 42: 42: 42: 42: There was 1 note 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 42: 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'spc-and-methanol' 42: 2 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.005 0.002 195.4 42: (ns/day) (hour/ns) 42: Performance: 111.173 0.216 42: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (10 ms) 42: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 42: Setting the LD random seed to -544245825 42: Generated 8 of the 10 non-bonded parameter combinations 42: Excluding 2 bonded neighbours molecule type 'Methanol' 42: Excluding 2 bonded neighbours molecule type 'SOL' 42: Number of degrees of freedom in T-Coupling group System is 12.00 42: 42: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 42: You are using a plain Coulomb cut-off, which might produce artifacts. 42: You might want to consider using PME electrostatics. 42: 42: 42: 42: There was 1 note 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 42: 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'spc-and-methanol' 42: 2 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.008 0.004 195.5 42: (ns/day) (hour/ns) 42: Performance: 64.975 0.369 42: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (53 ms) 42: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 42: Setting the LD random seed to -155461385 42: Generated 8 of the 10 non-bonded parameter combinations 42: Excluding 2 bonded neighbours molecule type 'Methanol' 42: Excluding 2 bonded neighbours molecule type 'SOL' 42: Number of degrees of freedom in T-Coupling group System is 12.00 42: 42: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: 42: You are using a plain Coulomb cut-off, which might produce artifacts. 42: You might want to consider using PME electrostatics. 42: 42: 42: 42: There was 1 note 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 42: 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'spc-and-methanol' 42: 2 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.007 0.004 194.9 42: (ns/day) (hour/ns) 42: Performance: 73.165 0.328 42: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (13 ms) 42: [----------] 3 tests from MdrunCanWrite/NptTrajectories (76 ms total) 42: 42: [----------] Global test environment tear-down 42: [==========] 12 tests from 5 test cases ran. (354 ms total) 42: [ PASSED ] 12 tests. 42/54 Test #42: MdrunOutputTests .................... Passed 0.37 sec test 43 Start 43: MdrunModulesTests 43: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/MdrunModulesTests.xml" 43: Test timeout computed to be: 600 43: [==========] Running 10 tests from 3 test cases. 43: [----------] Global test environment set-up. 43: [----------] 4 tests from DensityFittingTest 43: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct 43: Setting the LD random seed to -293240835 43: Generated 1 of the 1 non-bonded parameter combinations 43: Excluding 1 bonded neighbours molecule type 'Argon' 43: Number of degrees of freedom in T-Coupling group rest is 33.00 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: 43: Steepest Descents: 43: Tolerance (Fmax) = 1.00000e+01 43: Number of steps = 2 43: 43: Energy minimization reached the maximum number of steps before the forces 43: reached the requested precision Fmax < 10. 43: 43: writing lowest energy coordinates. 43: 43: Steepest Descents did not converge to Fmax < 10 in 3 steps. 43: Potential Energy = -3.8565400e+03 43: Maximum force = 2.8846870e+03 on atom 3 43: Norm of force = 1.0754448e+03 43: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as single precision energy file 43: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 This run will generate roughly 0 Mb of data 43: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (115 ms) 43: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy 43: Setting the LD random seed to -202133657 43: Generated 1 of the 1 non-bonded parameter combinations 43: Excluding 1 bonded neighbours molecule type 'Argon' 43: Number of degrees of freedom in T-Coupling group rest is 33.00 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: 43: Steepest Descents: 43: Tolerance (Fmax) = 1.00000e+01 43: Number of steps = 2 43: 43: Energy minimization reached the maximum number of steps before the forces 43: reached the requested precision Fmax < 10. 43: 43: writing lowest energy coordinates. 43: 43: Steepest Descents did not converge to Fmax < 10 in 3 steps. 43: Potential Energy = -2.7138666e+04 43: Maximum force = 4.3409717e+03 on atom 2 43: Norm of force = 1.2549793e+03 43: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as single precision energy file 43: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 This run will generate roughly 0 Mb of data 43: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (6 ms) 43: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch 43: 43: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:836:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. 43: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (7 ms) 43: [ RUN ] DensityFittingTest.CheckpointWorks 43: 43: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 43: Setting nstcalcenergy (100) equal to nstenergy (2) 43: 43: Setting the LD random seed to -536901643 43: Generated 1 of the 1 non-bonded parameter combinations 43: Excluding 1 bonded neighbours molecule type 'Argon' 43: Number of degrees of freedom in T-Coupling group rest is 33.00 43: 43: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 43: NVE simulation: will use the initial temperature of 68.810 K for 43: determining the Verlet buffer size 43: 43: 43: There were 2 notes 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 43: Can not increase nstlist because an NVE ensemble is used 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: starting mdrun 'Argon' 43: 2 steps, 0.0 ps. 43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K 43: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 43: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 43: Note that mdrun will redetermine rlist based on the actual pair-list setup 43: This run will generate roughly 0 Mb of data 43: 43: Writing final coordinates. 43: 43: Core t (s) Wall t (s) (%) 43: Time: 0.008 0.004 197.3 43: (ns/day) (hour/ns) 43: Performance: 63.196 0.380 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 43: 43: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps 43: Can not increase nstlist because an NVE ensemble is used 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: starting mdrun 'Argon' 43: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps). 43: 43: Writing final coordinates. 43: 43: Core t (s) Wall t (s) (%) 43: Time: 0.005 0.002 195.6 43: (ns/day) (hour/ns) 43: Performance: 187.281 0.128 43: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as single precision energy file 43: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (14 ms) 43: [----------] 4 tests from DensityFittingTest (142 ms total) 43: 43: [----------] 4 tests from MimicTest 43: [ RUN ] MimicTest.OneQuantumMol 43: 43: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 43: For a correct single-point energy evaluation with nsteps = 0, use 43: continuation = yes to avoid constraining the input coordinates. 43: 43: Setting the LD random seed to 860599547 43: Generated 10 of the 10 non-bonded parameter combinations 43: Generating 1-4 interactions: fudge = 0.5 43: Generated 10 of the 10 1-4 parameter combinations 43: Excluding 2 bonded neighbours molecule type 'SOL' 43: Number of degrees of freedom in T-Coupling group rest is 21.00 43: 43: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 43: NVE simulation with an initial temperature of zero: will use a Verlet 43: buffer of 10%. Check your energy drift! 43: 43: 43: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 43: You are using a plain Coulomb cut-off, which might produce artifacts. 43: You might want to consider using PME electrostatics. 43: 43: 43: 43: There were 3 notes 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 43: Can not increase nstlist because an NVE ensemble is used 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/4water.gro' 43: 43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 43: Reading frame 0 time 0.000 Last frame 0 time 0.000 43: 43: NOTE: 13 % of the run time was spent in pair search, 43: you might want to increase nstlist (this has no effect on accuracy) 43: 43: Core t (s) Wall t (s) (%) 43: Time: 0.001 0.000 186.6 43: (ns/day) (hour/ns) 43: Performance: 304.272 0.079 43: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 43: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 43: [ OK ] MimicTest.OneQuantumMol (6 ms) 43: [ RUN ] MimicTest.AllQuantumMol 43: 43: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 43: For a correct single-point energy evaluation with nsteps = 0, use 43: continuation = yes to avoid constraining the input coordinates. 43: 43: Setting the LD random seed to -301993985 43: Generated 10 of the 10 non-bonded parameter combinations 43: Generating 1-4 interactions: fudge = 0.5 43: Generated 10 of the 10 1-4 parameter combinations 43: Excluding 2 bonded neighbours molecule type 'SOL' 43: Number of degrees of freedom in T-Coupling group rest is 21.00 43: 43: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 43: NVE simulation with an initial temperature of zero: will use a Verlet 43: buffer of 10%. Check your energy drift! 43: 43: 43: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 43: You are using a plain Coulomb cut-off, which might produce artifacts. 43: You might want to consider using PME electrostatics. 43: 43: 43: 43: There were 3 notes 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 43: Can not increase nstlist because an NVE ensemble is used 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/4water.gro' 43: 43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 43: Reading frame 0 time 0.000 Last frame 0 time 0.000 43: 43: NOTE: 15 % of the run time was spent in pair search, 43: you might want to increase nstlist (this has no effect on accuracy) 43: 43: Core t (s) Wall t (s) (%) 43: Time: 0.001 0.000 187.3 43: (ns/day) (hour/ns) 43: Performance: 228.636 0.105 43: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 43: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 43: [ OK ] MimicTest.AllQuantumMol (15 ms) 43: [ RUN ] MimicTest.TwoQuantumMol 43: 43: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 43: For a correct single-point energy evaluation with nsteps = 0, use 43: continuation = yes to avoid constraining the input coordinates. 43: 43: Setting the LD random seed to -2361889 43: Generated 10 of the 10 non-bonded parameter combinations 43: Generating 1-4 interactions: fudge = 0.5 43: Generated 10 of the 10 1-4 parameter combinations 43: Excluding 2 bonded neighbours molecule type 'SOL' 43: Number of degrees of freedom in T-Coupling group rest is 21.00 43: 43: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 43: NVE simulation with an initial temperature of zero: will use a Verlet 43: buffer of 10%. Check your energy drift! 43: 43: 43: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 43: You are using a plain Coulomb cut-off, which might produce artifacts. 43: You might want to consider using PME electrostatics. 43: 43: 43: 43: There were 3 notes 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 43: Can not increase nstlist because an NVE ensemble is used 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/4water.gro' 43: 43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 43: Reading frame 0 time 0.000 Last frame 0 time 0.000 43: 43: NOTE: 17 % of the run time was spent in pair search, 43: you might want to increase nstlist (this has no effect on accuracy) 43: 43: Core t (s) Wall t (s) (%) 43: Time: 0.001 0.000 185.4 43: (ns/day) (hour/ns) 43: Performance: 262.410 0.091 43: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 43: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 43: [ OK ] MimicTest.TwoQuantumMol (9 ms) 43: [ RUN ] MimicTest.BondCuts 43: 43: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 43: For a correct single-point energy evaluation with nsteps = 0, use 43: continuation = yes to avoid constraining the input coordinates. 43: 43: Setting the LD random seed to -134369813 43: Generated 2211 of the 2211 non-bonded parameter combinations 43: Generating 1-4 interactions: fudge = 0.5 43: Generated 2211 of the 2211 1-4 parameter combinations 43: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 43: Number of degrees of freedom in T-Coupling group rest is 66.00 43: 43: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 43: NVE simulation: will use the initial temperature of 300.368 K for 43: determining the Verlet buffer size 43: 43: 43: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 43: You are using a plain Coulomb cut-off, which might produce artifacts. 43: You might want to consider using PME electrostatics. 43: 43: 43: 43: There were 3 notes 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 43: Can not increase nstlist because an NVE ensemble is used 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/ala.gro' 43: 43: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 43: Reading frame 0 time 0.000 Last frame 0 time 0.000 43: 43: NOTE: 17 % of the run time was spent in pair search, 43: you might want to increase nstlist (this has no effect on accuracy) 43: 43: Core t (s) Wall t (s) (%) 43: Time: 0.001 0.000 190.0 43: (ns/day) (hour/ns) 43: Performance: 207.672 0.116 43: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 43: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 43: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm 43: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm 43: Note that mdrun will redetermine rlist based on the actual pair-list setup 43: This run will generate roughly 0 Mb of data 43: [ OK ] MimicTest.BondCuts (18 ms) 43: [----------] 4 tests from MimicTest (49 ms total) 43: 43: [----------] 2 tests from WithIntegrator/ImdTest 43: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0 43: Setting the LD random seed to 1528739711 43: Generated 20503 of the 20503 non-bonded parameter combinations 43: Generating 1-4 interactions: fudge = 1 43: Generated 17396 of the 20503 1-4 parameter combinations 43: Excluding 3 bonded neighbours molecule type 'Glycine' 43: 43: NOTE 1 [file glycine_vacuo.top, line 12]: 43: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an 43: estimated oscillational period of 1.0e-02 ps, which is less than 10 times 43: the time step of 2.0e-03 ps. 43: Maybe you forgot to change the constraints mdp option. 43: 43: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 43: Number of degrees of freedom in T-Coupling group System is 27.00 43: 43: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]: 43: You are using a plain Coulomb cut-off, which might produce artifacts. 43: You might want to consider using PME electrostatics. 43: 43: 43: 43: There were 2 notes 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 43: Changing nstlist from 10 to 50, rlist from 1.026 to 1.34 43: 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: IMD: Enabled. This simulation will accept incoming IMD connections. 43: IMD: Pulling from IMD remote is enabled (-imdpull). 43: IMD: Setting port for connection requests to 0. 43: IMD: Setting up incoming socket. 43: IMD: Listening for IMD connection on port 54887. 43: IMD: -imdwait not set, starting simulation. 43: starting mdrun 'Glycine' 43: 2 steps, 0.0 ps. 43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 43: Set rlist, assuming 4x4 atom pair-list, to 1.026 nm, buffer size 0.026 nm 43: Note that mdrun will redetermine rlist based on the actual pair-list setup 43: This run will generate roughly 0 Mb of data 43: 43: Writing final coordinates. 43: 43: Core t (s) Wall t (s) (%) 43: Time: 0.019 0.009 197.0 43: (ns/day) (hour/ns) 43: Performance: 54.581 0.440 43: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (198 ms) 43: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1 43: 43: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 43: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not 43: apply to steep. 43: 43: Setting the LD random seed to -1756104705 43: Generated 20503 of the 20503 non-bonded parameter combinations 43: Generating 1-4 interactions: fudge = 1 43: Generated 17396 of the 20503 1-4 parameter combinations 43: Excluding 3 bonded neighbours molecule type 'Glycine' 43: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 43: Number of degrees of freedom in T-Coupling group System is 27.00 43: 43: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 43: You are using a plain Coulomb cut-off, which might produce artifacts. 43: You might want to consider using PME electrostatics. 43: 43: 43: 43: There were 2 notes 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: IMD: Enabled. This simulation will accept incoming IMD connections. 43: IMD: Pulling from IMD remote is enabled (-imdpull). 43: IMD: Setting port for connection requests to 0. 43: IMD: Setting up incoming socket. 43: IMD: Listening for IMD connection on port 37241. 43: IMD: -imdwait not set, starting simulation. 43: 43: Steepest Descents: 43: Tolerance (Fmax) = 1.00000e+01 43: Number of steps = 2 43: 43: Energy minimization reached the maximum number of steps before the forces 43: reached the requested precision Fmax < 10. 43: 43: writing lowest energy coordinates. 43: 43: Steepest Descents did not converge to Fmax < 10 in 3 steps. 43: Potential Energy = 1.1977063e+03 43: Maximum force = 1.7794877e+04 on atom 9 43: Norm of force = 7.8732901e+03 43: This run will generate roughly 0 Mb of data 43: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (281 ms) 43: [----------] 2 tests from WithIntegrator/ImdTest (479 ms total) 43: 43: [----------] Global test environment tear-down 43: [==========] 10 tests from 3 test cases ran. (670 ms total) 43: [ PASSED ] 10 tests. 43/54 Test #43: MdrunModulesTests ................... Passed 0.69 sec test 44 Start 44: MdrunIOTests 44: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/MdrunIOTests.xml" 44: Test timeout computed to be: 600 44: [==========] Running 51 tests from 9 test cases. 44: [----------] Global test environment set-up. 44: [----------] 3 tests from GromppTest 44: [ RUN ] GromppTest.EmptyMdpFileWorks 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 44: For a correct single-point energy evaluation with nsteps = 0, use 44: continuation = yes to avoid constraining the input coordinates. 44: 44: Setting the LD random seed to -539007116 44: Generated 8 of the 10 non-bonded parameter combinations 44: Excluding 2 bonded neighbours molecule type 'Methanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group rest is 12.00 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 44: NVE simulation: will use the initial temperature of 1046.791 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 44: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: [ OK ] GromppTest.EmptyMdpFileWorks (4 ms) 44: [ RUN ] GromppTest.SimulatedAnnealingWorks 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 44: For a correct single-point energy evaluation with nsteps = 0, use 44: continuation = yes to avoid constraining the input coordinates. 44: 44: Setting the LD random seed to -438337665 44: Generated 8 of the 10 non-bonded parameter combinations 44: Excluding 2 bonded neighbours molecule type 'Methanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Simulated annealing for group rest: Periodic, 4 timepoints 44: Time (ps) Temperature (K) 44: 0.0 298.0 44: 2.0 320.0 44: 4.0 320.0 44: 6.0 298.0 44: Number of degrees of freedom in T-Coupling group rest is 12.00 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 44: NVE simulation: will use the initial temperature of 1046.791 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 44: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: [ OK ] GromppTest.SimulatedAnnealingWorks (4 ms) 44: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 44: For a correct single-point energy evaluation with nsteps = 0, use 44: continuation = yes to avoid constraining the input coordinates. 44: 44: Setting the LD random seed to -26412634 44: Generated 8 of the 10 non-bonded parameter combinations 44: Excluding 2 bonded neighbours molecule type 'Methanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Simulated annealing for group Methanol: Single, 3 timepoints 44: Time (ps) Temperature (K) 44: 0.0 298.0 44: 3.0 280.0 44: 6.0- 270.0 44: Simulated annealing for group SOL: Periodic, 4 timepoints 44: Time (ps) Temperature (K) 44: 0.0 298.0 44: 2.0 320.0 44: 4.0 320.0 44: 6.0 298.0 44: Number of degrees of freedom in T-Coupling group Methanol is 7.20 44: Number of degrees of freedom in T-Coupling group SOL is 4.80 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 44: NVE simulation: will use the initial temperature of 1046.791 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 44: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (4 ms) 44: [----------] 3 tests from GromppTest (12 ms total) 44: 44: [----------] 6 tests from MdrunTerminationTest 44: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault 44: Setting the LD random seed to 2134376409 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There was 1 note 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 2 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.012 0.006 197.4 44: (ns/day) (hour/ns) 44: Performance: 41.435 0.579 44: Reading toplogy and stuff from /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Setting nsteps to 4 44: Writing statusfile with starting step 0 and length 4 steps... 44: time 0.000 and length 0.004 ps 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.002 190.6 44: (ns/day) (hour/ns) 44: Performance: 170.162 0.141 44: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (107 ms) 44: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 44: Setting the LD random seed to -687891073 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There was 1 note 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 10 to 1, rlist from 1.024 to 1 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 100 steps, 0.1 ps. 44: 44: Step 6: Run time exceeded 0.000 hours, will terminate the run within 2 steps 44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.080 0.040 199.5 44: (ns/day) (hour/ns) 44: Performance: 17.232 1.393 44: Reading toplogy and stuff from /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Setting nsteps to 102 44: Writing statusfile with starting step 0 and length 102 steps... 44: time 0.000 and length 0.102 ps 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 102 steps, 0.1 ps (continuing from step 7, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.011 0.005 197.7 44: (ns/day) (hour/ns) 44: Performance: 1525.442 0.016 44: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (58 ms) 44: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend 44: Setting the LD random seed to 1606671843 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There was 1 note 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 2 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.004 0.002 192.8 44: (ns/day) (hour/ns) 44: Performance: 125.134 0.192 44: Reading toplogy and stuff from /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Setting nsteps to 4 44: Writing statusfile with starting step 0 and length 4 steps... 44: time 0.000 and length 0.004 ps 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.004 0.002 198.2 44: (ns/day) (hour/ns) 44: Performance: 138.105 0.174 44: Reading toplogy and stuff from /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Setting nsteps to 6 44: Writing statusfile with starting step 0 and length 6 steps... 44: time 0.000 and length 0.006 ps 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.002 197.8 44: (ns/day) (hour/ns) 44: Performance: 108.705 0.221 44: Reading toplogy and stuff from /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Setting nsteps to 8 44: Writing statusfile with starting step 0 and length 8 steps... 44: time 0.000 and length 0.008 ps 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.002 198.0 44: (ns/day) (hour/ns) 44: Performance: 109.914 0.218 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: NOTE: 20 % of the run time was spent in pair search, 44: you might want to increase nstlist (this has no effect on accuracy) 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.000 0.000 174.3 44: (ns/day) (hour/ns) 44: Performance: 452.419 0.053 44: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (29 ms) 44: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile 44: Setting the LD random seed to -76080289 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There was 1 note 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 2 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.010 0.005 196.3 44: (ns/day) (hour/ns) 44: Performance: 50.222 0.478 44: Reading toplogy and stuff from /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Setting nsteps to 4 44: Writing statusfile with starting step 0 and length 4 steps... 44: time 0.000 and length 0.004 ps 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 4 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.003 193.7 44: (ns/day) (hour/ns) 44: Performance: 162.099 0.148 44: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (72 ms) 44: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile 44: Setting the LD random seed to 1475852265 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There was 1 note 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 2 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.003 194.5 44: (ns/day) (hour/ns) 44: Performance: 97.181 0.247 44: Reading toplogy and stuff from /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Setting nsteps to 4 44: Writing statusfile with starting step 0 and length 4 steps... 44: time 0.000 and length 0.004 ps 44: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (12 ms) 44: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles 44: Setting the LD random seed to 1607278463 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There was 1 note 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 2 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.004 0.002 193.3 44: (ns/day) (hour/ns) 44: Performance: 113.483 0.211 44: Reading toplogy and stuff from /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Setting nsteps to 4 44: Writing statusfile with starting step 0 and length 4 steps... 44: time 0.000 and length 0.004 ps 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.003 197.8 44: (ns/day) (hour/ns) 44: Performance: 102.264 0.235 44: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (19 ms) 44: [----------] 6 tests from MdrunTerminationTest (297 ms total) 44: 44: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.095 0.048 199.6 44: (ns/day) (hour/ns) 44: Performance: 30.760 0.780 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.008 0.004 196.8 44: (ns/day) (hour/ns) 44: Performance: 197.307 0.122 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.007 0.003 195.7 44: (ns/day) (hour/ns) 44: Performance: 224.173 0.107 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (74 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.009 0.004 198.0 44: (ns/day) (hour/ns) 44: Performance: 341.269 0.070 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.007 0.003 198.7 44: (ns/day) (hour/ns) 44: Performance: 225.194 0.107 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.007 0.003 198.2 44: (ns/day) (hour/ns) 44: Performance: 233.882 0.103 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (30 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.010 0.005 196.0 44: (ns/day) (hour/ns) 44: Performance: 302.390 0.079 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.003 196.8 44: (ns/day) (hour/ns) 44: Performance: 307.949 0.078 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.002 196.9 44: (ns/day) (hour/ns) 44: Performance: 315.455 0.076 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (80 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.006 0.003 197.0 44: (ns/day) (hour/ns) 44: Performance: 457.119 0.053 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.085 0.043 199.3 44: (ns/day) (hour/ns) 44: Performance: 18.172 1.321 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.037 0.019 197.9 44: (ns/day) (hour/ns) 44: Performance: 41.178 0.583 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (83 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: NVE simulation: will use the initial temperature of 2573.591 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 4 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: NVE simulation: will use the initial temperature of 2573.591 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 4 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.019 0.010 198.2 44: (ns/day) (hour/ns) 44: Performance: 149.787 0.160 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.011 0.006 196.1 44: (ns/day) (hour/ns) 44: Performance: 138.698 0.173 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.093 0.047 199.6 44: (ns/day) (hour/ns) 44: Performance: 16.703 1.437 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (97 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: NVE simulation: will use the initial temperature of 2573.591 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 4 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: NVE simulation: will use the initial temperature of 2573.591 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 4 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.007 0.004 198.4 44: (ns/day) (hour/ns) 44: Performance: 400.039 0.060 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.009 0.005 198.0 44: (ns/day) (hour/ns) 44: Performance: 168.023 0.143 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.009 0.005 198.7 44: (ns/day) (hour/ns) 44: Performance: 170.741 0.141 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (34 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.006 0.003 195.4 44: (ns/day) (hour/ns) 44: Performance: 449.711 0.053 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.024 0.012 198.6 44: (ns/day) (hour/ns) 44: Performance: 64.051 0.375 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.019 0.009 198.0 44: (ns/day) (hour/ns) 44: Performance: 82.720 0.290 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (84 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.015 0.008 197.7 44: (ns/day) (hour/ns) 44: Performance: 187.480 0.128 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.017 0.008 198.2 44: (ns/day) (hour/ns) 44: Performance: 92.091 0.261 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.010 0.005 196.4 44: (ns/day) (hour/ns) 44: Performance: 153.996 0.156 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (37 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2145 of the 2145 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2145 of the 2145 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 44: 44: NOTE 3 [file unknown]: 44: You are using constraints on all bonds, whereas the forcefield has been 44: parametrized only with constraints involving hydrogen atoms. We suggest 44: using constraints = h-bonds instead, this will also improve performance. 44: 44: Cleaning up constraints and constant bonded interactions with virtual sites 44: Removed 18 Angles with virtual sites, 21 left 44: Removed 10 Proper Dih.s with virtual sites, 44 left 44: Converted 15 Constraints with virtual sites to connections, 7 left 44: Number of degrees of freedom in T-Coupling group System is 23.00 44: 44: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: NVE simulation: will use the initial temperature of 456.887 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 5 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: There are 9 non-linear virtual site constructions. Their contribution to 44: the energy error is approximated. In most cases this does not affect the 44: error significantly. 44: 44: 44: NOTE 6 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 6 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2145 of the 2145 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2145 of the 2145 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 44: 44: NOTE 3 [file unknown]: 44: You are using constraints on all bonds, whereas the forcefield has been 44: parametrized only with constraints involving hydrogen atoms. We suggest 44: using constraints = h-bonds instead, this will also improve performance. 44: 44: Cleaning up constraints and constant bonded interactions with virtual sites 44: Removed 18 Angles with virtual sites, 21 left 44: Removed 10 Proper Dih.s with virtual sites, 44 left 44: Converted 15 Constraints with virtual sites to connections, 7 left 44: Number of degrees of freedom in T-Coupling group System is 23.00 44: 44: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: NVE simulation: will use the initial temperature of 456.887 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 5 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: There are 9 non-linear virtual site constructions. Their contribution to 44: the energy error is approximated. In most cases this does not affect the 44: error significantly. 44: 44: 44: NOTE 6 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 6 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 16 steps, 0.0 ps. 44: turning all bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: turning all bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.027 0.014 198.0 44: (ns/day) (hour/ns) 44: Performance: 108.132 0.222 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.008 0.004 196.7 44: (ns/day) (hour/ns) 44: Performance: 194.867 0.123 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.064 0.032 199.1 44: (ns/day) (hour/ns) 44: Performance: 24.237 0.990 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (137 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2145 of the 2145 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2145 of the 2145 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 44: 44: NOTE 3 [file unknown]: 44: You are using constraints on all bonds, whereas the forcefield has been 44: parametrized only with constraints involving hydrogen atoms. We suggest 44: using constraints = h-bonds instead, this will also improve performance. 44: 44: Cleaning up constraints and constant bonded interactions with virtual sites 44: Removed 18 Angles with virtual sites, 21 left 44: Removed 10 Proper Dih.s with virtual sites, 44 left 44: Converted 15 Constraints with virtual sites to connections, 7 left 44: Number of degrees of freedom in T-Coupling group System is 23.00 44: 44: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: NVE simulation: will use the initial temperature of 456.887 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 5 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: There are 9 non-linear virtual site constructions. Their contribution to 44: the energy error is approximated. In most cases this does not affect the 44: error significantly. 44: 44: 44: NOTE 6 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 6 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2145 of the 2145 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2145 of the 2145 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 44: 44: NOTE 3 [file unknown]: 44: You are using constraints on all bonds, whereas the forcefield has been 44: parametrized only with constraints involving hydrogen atoms. We suggest 44: using constraints = h-bonds instead, this will also improve performance. 44: 44: Cleaning up constraints and constant bonded interactions with virtual sites 44: Removed 18 Angles with virtual sites, 21 left 44: Removed 10 Proper Dih.s with virtual sites, 44 left 44: Converted 15 Constraints with virtual sites to connections, 7 left 44: Number of degrees of freedom in T-Coupling group System is 23.00 44: 44: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: NVE simulation: will use the initial temperature of 456.887 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 5 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: There are 9 non-linear virtual site constructions. Their contribution to 44: the energy error is approximated. In most cases this does not affect the 44: error significantly. 44: 44: 44: NOTE 6 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 6 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 16 steps, 0.0 ps. 44: turning all bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: turning all bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.010 0.005 197.1 44: (ns/day) (hour/ns) 44: Performance: 280.142 0.086 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.006 0.003 196.0 44: (ns/day) (hour/ns) 44: Performance: 243.959 0.098 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.017 0.009 197.2 44: (ns/day) (hour/ns) 44: Performance: 88.125 0.272 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (108 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2145 of the 2145 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2145 of the 2145 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 44: 44: NOTE 3 [file unknown]: 44: You are using constraints on all bonds, whereas the forcefield has been 44: parametrized only with constraints involving hydrogen atoms. We suggest 44: using constraints = h-bonds instead, this will also improve performance. 44: 44: Cleaning up constraints and constant bonded interactions with virtual sites 44: Removed 18 Angles with virtual sites, 21 left 44: Removed 10 Proper Dih.s with virtual sites, 44 left 44: Converted 15 Constraints with virtual sites to connections, 7 left 44: Number of degrees of freedom in T-Coupling group System is 23.00 44: 44: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 44: There are 9 non-linear virtual site constructions. Their contribution to 44: the energy error is approximated. In most cases this does not affect the 44: error significantly. 44: 44: 44: NOTE 5 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 5 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2145 of the 2145 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2145 of the 2145 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 44: 44: NOTE 3 [file unknown]: 44: You are using constraints on all bonds, whereas the forcefield has been 44: parametrized only with constraints involving hydrogen atoms. We suggest 44: using constraints = h-bonds instead, this will also improve performance. 44: 44: Cleaning up constraints and constant bonded interactions with virtual sites 44: Removed 18 Angles with virtual sites, 21 left 44: Removed 10 Proper Dih.s with virtual sites, 44 left 44: Converted 15 Constraints with virtual sites to connections, 7 left 44: Number of degrees of freedom in T-Coupling group System is 23.00 44: 44: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 44: There are 9 non-linear virtual site constructions. Their contribution to 44: the energy error is approximated. In most cases this does not affect the 44: error significantly. 44: 44: 44: NOTE 5 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 5 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 16 steps, 0.0 ps. 44: turning all bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: turning all bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.019 0.009 197.5 44: (ns/day) (hour/ns) 44: Performance: 155.351 0.154 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.010 0.005 195.3 44: (ns/day) (hour/ns) 44: Performance: 158.371 0.152 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.010 0.005 195.8 44: (ns/day) (hour/ns) 44: Performance: 155.088 0.155 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (140 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2145 of the 2145 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2145 of the 2145 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 44: 44: NOTE 3 [file unknown]: 44: You are using constraints on all bonds, whereas the forcefield has been 44: parametrized only with constraints involving hydrogen atoms. We suggest 44: using constraints = h-bonds instead, this will also improve performance. 44: 44: Cleaning up constraints and constant bonded interactions with virtual sites 44: Removed 18 Angles with virtual sites, 21 left 44: Removed 10 Proper Dih.s with virtual sites, 44 left 44: Converted 15 Constraints with virtual sites to connections, 7 left 44: Number of degrees of freedom in T-Coupling group System is 23.00 44: 44: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 44: There are 9 non-linear virtual site constructions. Their contribution to 44: the energy error is approximated. In most cases this does not affect the 44: error significantly. 44: 44: 44: NOTE 5 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 5 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2145 of the 2145 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2145 of the 2145 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 44: 44: NOTE 3 [file unknown]: 44: You are using constraints on all bonds, whereas the forcefield has been 44: parametrized only with constraints involving hydrogen atoms. We suggest 44: using constraints = h-bonds instead, this will also improve performance. 44: 44: Cleaning up constraints and constant bonded interactions with virtual sites 44: Removed 18 Angles with virtual sites, 21 left 44: Removed 10 Proper Dih.s with virtual sites, 44 left 44: Converted 15 Constraints with virtual sites to connections, 7 left 44: Number of degrees of freedom in T-Coupling group System is 23.00 44: 44: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 44: There are 9 non-linear virtual site constructions. Their contribution to 44: the energy error is approximated. In most cases this does not affect the 44: error significantly. 44: 44: 44: NOTE 5 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 5 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 16 steps, 0.0 ps. 44: turning all bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: turning all bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.012 0.006 197.5 44: (ns/day) (hour/ns) 44: Performance: 233.719 0.103 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.078 0.039 199.4 44: (ns/day) (hour/ns) 44: Performance: 19.878 1.207 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.011 0.006 196.0 44: (ns/day) (hour/ns) 44: Performance: 136.384 0.176 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (166 ms) 44: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (1070 ms total) 44: 44: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact 44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2485 of the 2485 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2485 of the 2485 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'nonanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 79.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: NVE simulation: will use the initial temperature of 293.480 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 4 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2485 of the 2485 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2485 of the 2485 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'nonanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 79.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: NVE simulation: will use the initial temperature of 293.480 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 4 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 16 steps, 0.0 ps. 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.018 0.009 197.3 44: (ns/day) (hour/ns) 44: Performance: 162.373 0.148 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.010 0.005 194.7 44: (ns/day) (hour/ns) 44: Performance: 155.963 0.154 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.009 0.005 196.7 44: (ns/day) (hour/ns) 44: Performance: 169.905 0.141 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (114 ms) 44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2485 of the 2485 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2485 of the 2485 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'nonanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 79.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: NVE simulation: will use the initial temperature of 293.480 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 4 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2485 of the 2485 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2485 of the 2485 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'nonanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 79.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: NVE simulation: will use the initial temperature of 293.480 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 4 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 16 steps, 0.0 ps. 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.033 0.017 199.3 44: (ns/day) (hour/ns) 44: Performance: 88.142 0.272 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.013 0.006 198.1 44: (ns/day) (hour/ns) 44: Performance: 120.412 0.199 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.012 0.006 198.6 44: (ns/day) (hour/ns) 44: Performance: 125.679 0.191 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (108 ms) 44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2485 of the 2485 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2485 of the 2485 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'nonanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 79.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2485 of the 2485 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2485 of the 2485 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'nonanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 79.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 16 steps, 0.0 ps. 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.015 0.007 195.9 44: (ns/day) (hour/ns) 44: Performance: 197.525 0.122 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.007 0.004 194.0 44: (ns/day) (hour/ns) 44: Performance: 213.924 0.112 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.014 0.007 197.4 44: (ns/day) (hour/ns) 44: Performance: 109.266 0.220 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (171 ms) 44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2485 of the 2485 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2485 of the 2485 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'nonanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 79.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2485 of the 2485 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2485 of the 2485 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'nonanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 79.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 16 steps, 0.0 ps. 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.013 0.007 197.2 44: (ns/day) (hour/ns) 44: Performance: 215.888 0.111 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.012 0.006 190.8 44: (ns/day) (hour/ns) 44: Performance: 125.192 0.192 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.010 0.005 195.9 44: (ns/day) (hour/ns) 44: Performance: 147.866 0.162 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (122 ms) 44: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (515 ms total) 44: 44: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact 44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.003 194.5 44: (ns/day) (hour/ns) 44: Performance: 571.378 0.042 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.007 0.004 197.3 44: (ns/day) (hour/ns) 44: Performance: 211.442 0.114 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.109 0.055 199.8 44: (ns/day) (hour/ns) 44: Performance: 14.217 1.688 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (77 ms) 44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.014 0.007 198.0 44: (ns/day) (hour/ns) 44: Performance: 209.387 0.115 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.006 0.003 195.5 44: (ns/day) (hour/ns) 44: Performance: 250.345 0.096 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.007 0.003 195.9 44: (ns/day) (hour/ns) 44: Performance: 224.775 0.107 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (34 ms) 44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.007 0.004 195.1 44: (ns/day) (hour/ns) 44: Performance: 415.274 0.058 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.015 0.007 197.7 44: (ns/day) (hour/ns) 44: Performance: 104.005 0.231 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.014 0.007 197.9 44: (ns/day) (hour/ns) 44: Performance: 109.992 0.218 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (76 ms) 44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.003 196.7 44: (ns/day) (hour/ns) 44: Performance: 566.648 0.042 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.004 0.002 194.3 44: (ns/day) (hour/ns) 44: Performance: 356.058 0.067 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.004 0.002 196.6 44: (ns/day) (hour/ns) 44: Performance: 375.878 0.064 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (20 ms) 44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.006 0.003 198.2 44: (ns/day) (hour/ns) 44: Performance: 527.584 0.045 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.100 0.050 199.8 44: (ns/day) (hour/ns) 44: Performance: 15.536 1.545 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.014 0.007 198.7 44: (ns/day) (hour/ns) 44: Performance: 114.134 0.210 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (78 ms) 44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.010 0.005 197.7 44: (ns/day) (hour/ns) 44: Performance: 283.598 0.085 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.007 0.004 193.4 44: (ns/day) (hour/ns) 44: Performance: 201.439 0.119 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.006 0.003 197.1 44: (ns/day) (hour/ns) 44: Performance: 239.974 0.100 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (32 ms) 44: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact (317 ms total) 44: 44: [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact 44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.010 0.005 196.4 44: (ns/day) (hour/ns) 44: Performance: 290.088 0.083 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.006 0.003 194.1 44: (ns/day) (hour/ns) 44: Performance: 252.145 0.095 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.006 0.003 195.9 44: (ns/day) (hour/ns) 44: Performance: 255.603 0.094 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (82 ms) 44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.006 0.003 196.2 44: (ns/day) (hour/ns) 44: Performance: 456.138 0.053 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.006 0.003 195.8 44: (ns/day) (hour/ns) 44: Performance: 274.006 0.088 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.007 0.003 195.9 44: (ns/day) (hour/ns) 44: Performance: 226.069 0.106 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (73 ms) 44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.008 0.004 197.0 44: (ns/day) (hour/ns) 44: Performance: 349.775 0.069 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.006 0.003 196.4 44: (ns/day) (hour/ns) 44: Performance: 264.302 0.091 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.007 0.004 195.0 44: (ns/day) (hour/ns) 44: Performance: 218.995 0.110 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (29 ms) 44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.008 0.004 196.2 44: (ns/day) (hour/ns) 44: Performance: 382.195 0.063 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.007 0.004 197.4 44: (ns/day) (hour/ns) 44: Performance: 214.939 0.112 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.106 0.053 199.8 44: (ns/day) (hour/ns) 44: Performance: 14.617 1.642 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (76 ms) 44: [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact (261 ms total) 44: 44: [----------] 12 tests from NPT/MdrunNoAppendContinuationIsExact 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.008 0.004 197.0 44: (ns/day) (hour/ns) 44: Performance: 343.151 0.070 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.003 196.4 44: (ns/day) (hour/ns) 44: Performance: 281.115 0.085 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.008 0.004 196.6 44: (ns/day) (hour/ns) 44: Performance: 195.486 0.123 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (31 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.007 0.003 197.2 44: (ns/day) (hour/ns) 44: Performance: 440.893 0.054 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.006 0.003 196.0 44: (ns/day) (hour/ns) 44: Performance: 273.294 0.088 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.026 0.013 198.4 44: (ns/day) (hour/ns) 44: Performance: 60.305 0.398 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (77 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.007 0.003 196.1 44: (ns/day) (hour/ns) 44: Performance: 427.641 0.056 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.007 0.003 195.6 44: (ns/day) (hour/ns) 44: Performance: 230.951 0.104 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.012 0.006 196.1 44: (ns/day) (hour/ns) 44: Performance: 128.806 0.186 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (32 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.010 0.005 197.3 44: (ns/day) (hour/ns) 44: Performance: 295.571 0.081 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.013 0.007 198.1 44: (ns/day) (hour/ns) 44: Performance: 119.289 0.201 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.007 0.003 194.7 44: (ns/day) (hour/ns) 44: Performance: 228.348 0.105 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (76 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 44: 44: 44: WARNING 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: Using Berendsen pressure coupling invalidates the true ensemble for the 44: thermostat 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: 44: There was 1 warning 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 44: 44: 44: WARNING 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: Using Berendsen pressure coupling invalidates the true ensemble for the 44: thermostat 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: 44: There was 1 warning 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.006 0.003 195.3 44: (ns/day) (hour/ns) 44: Performance: 447.425 0.054 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.007 0.003 195.3 44: (ns/day) (hour/ns) 44: Performance: 226.886 0.106 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.009 0.005 197.3 44: (ns/day) (hour/ns) 44: Performance: 165.979 0.145 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (87 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.007 0.004 195.5 44: (ns/day) (hour/ns) 44: Performance: 406.345 0.059 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.006 0.003 194.5 44: (ns/day) (hour/ns) 44: Performance: 250.556 0.096 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.008 0.004 196.6 44: (ns/day) (hour/ns) 44: Performance: 193.262 0.124 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (27 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.006 0.003 197.2 44: (ns/day) (hour/ns) 44: Performance: 476.052 0.050 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.006 0.003 197.1 44: (ns/day) (hour/ns) 44: Performance: 275.883 0.087 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.009 0.005 196.5 44: (ns/day) (hour/ns) 44: Performance: 167.608 0.143 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (73 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 44: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (0 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.009 0.004 196.2 44: (ns/day) (hour/ns) 44: Performance: 337.437 0.071 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.003 196.4 44: (ns/day) (hour/ns) 44: Performance: 302.242 0.079 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.003 194.6 44: (ns/day) (hour/ns) 44: Performance: 298.262 0.080 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (28 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.098 0.049 199.8 44: (ns/day) (hour/ns) 44: Performance: 29.949 0.801 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.010 0.005 198.1 44: (ns/day) (hour/ns) 44: Performance: 147.860 0.162 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.007 0.004 198.2 44: (ns/day) (hour/ns) 44: Performance: 209.850 0.114 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (78 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10 44: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (0 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11 44: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (0 ms) 44: [----------] 12 tests from NPT/MdrunNoAppendContinuationIsExact (509 ms total) 44: 44: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact 44: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.010 0.005 197.9 44: (ns/day) (hour/ns) 44: Performance: 281.988 0.085 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.003 196.8 44: (ns/day) (hour/ns) 44: Performance: 301.320 0.080 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.003 196.9 44: (ns/day) (hour/ns) 44: Performance: 289.936 0.083 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (28 ms) 44: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (28 ms total) 44: 44: [----------] 3 tests from Checking/InitialConstraintsTest 44: [ RUN ] Checking/InitialConstraintsTest.Works/0 44: Setting the LD random seed to -1812070617 44: Generated 8 of the 10 non-bonded parameter combinations 44: Excluding 2 bonded neighbours molecule type 'Methanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group rest is 11.00 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 44: NVE simulation: will use the initial temperature of 1141.954 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc-and-methanol' 44: 1 steps, 0.0 ps. 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 44: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.004 0.002 189.7 44: (ns/day) (hour/ns) 44: Performance: 79.593 0.302 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (9 ms) 44: [ RUN ] Checking/InitialConstraintsTest.Works/1 44: Setting the LD random seed to -26666187 44: Generated 8 of the 10 non-bonded parameter combinations 44: Excluding 2 bonded neighbours molecule type 'Methanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group rest is 11.00 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 44: NVE simulation: will use the initial temperature of 1141.954 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc-and-methanol' 44: 1 steps, 0.0 ps. 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 44: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.010 0.005 197.9 44: (ns/day) (hour/ns) 44: Performance: 34.105 0.704 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (53 ms) 44: [ RUN ] Checking/InitialConstraintsTest.Works/2 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 44: Integrator method md-vv-avek is implemented primarily for validation 44: purposes; for molecular dynamics, you should probably be using md or md-vv 44: 44: Setting the LD random seed to -705691846 44: Generated 8 of the 10 non-bonded parameter combinations 44: Excluding 2 bonded neighbours molecule type 'Methanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group rest is 11.00 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 44: NVE simulation: will use the initial temperature of 1141.954 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc-and-methanol' 44: 1 steps, 0.0 ps. 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 44: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.003 193.2 44: (ns/day) (hour/ns) 44: Performance: 66.781 0.359 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as single precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (13 ms) 44: [----------] 3 tests from Checking/InitialConstraintsTest (75 ms total) 44: 44: [----------] Global test environment tear-down 44: [==========] 51 tests from 9 test cases ran. (3085 ms total) 44: [ PASSED ] 51 tests. 44/54 Test #44: MdrunIOTests ........................ Passed 3.11 sec test 45 Start 45: MdrunTests 45: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/mdrun-test "-ntomp" "2" "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/MdrunTests.xml" 45: Test timeout computed to be: 600 45: [==========] Running 12 tests from 5 test cases. 45: [----------] Global test environment set-up. 45: [----------] 1 test from DispersionCorrectionTest 45: [ RUN ] DispersionCorrectionTest.DispersionCorrectionCanRun 45: 45: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 45: The Berendsen thermostat does not generate the correct kinetic energy 45: distribution. You might want to consider using the V-rescale thermostat. 45: 45: Setting the LD random seed to -1073779716 45: Generated 2145 of the 2145 non-bonded parameter combinations 45: Generating 1-4 interactions: fudge = 0.5 45: Generated 2145 of the 2145 1-4 parameter combinations 45: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 45: Cleaning up constraints and constant bonded interactions with virtual sites 45: Converted 3 Bonds with virtual sites to connections, 7 left 45: Removed 18 Angles with virtual sites, 21 left 45: Removed 10 Proper Dih.s with virtual sites, 44 left 45: Converted 12 Constraints with virtual sites to connections, 0 left 45: Number of degrees of freedom in T-Coupling group System is 30.00 45: 45: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 45: There are 9 non-linear virtual site constructions. Their contribution to 45: the energy error is approximated. In most cases this does not affect the 45: error significantly. 45: 45: 45: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 45: You are using a plain Coulomb cut-off, which might produce artifacts. 45: You might want to consider using PME electrostatics. 45: 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 45: Changing nstlist from 10 to 50, rlist from 1.016 to 1.167 45: 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'Alanine dipeptide in vacuo' 45: 200 steps, 0.4 ps. 45: turning H bonds into constraints... 45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 45: Calculated rlist for 1x1 atom pair-list as 1.028 nm, buffer size 0.028 nm 45: Set rlist, assuming 4x4 atom pair-list, to 1.016 nm, buffer size 0.016 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: This run will generate roughly 0 Mb of data 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.046 0.023 199.3 45: (ns/day) (hour/ns) 45: Performance: 1510.372 0.016 45: [ OK ] DispersionCorrectionTest.DispersionCorrectionCanRun (171 ms) 45: [----------] 1 test from DispersionCorrectionTest (171 ms total) 45: 45: [----------] 1 test from OriresTest 45: [ RUN ] OriresTest.OriresCanRun 45: 45: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: 45: The Berendsen thermostat does not generate the correct kinetic energy 45: distribution. You might want to consider using the V-rescale thermostat. 45: 45: Setting the LD random seed to 531733487 45: Generated 2145 of the 2145 non-bonded parameter combinations 45: Generating 1-4 interactions: fudge = 0.5 45: Generated 2145 of the 2145 1-4 parameter combinations 45: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 45: Excluding 2 bonded neighbours molecule type 'SOL' 45: Number of degrees of freedom in T-Coupling group System is 518.00 45: 45: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: 45: You are using a plain Coulomb cut-off, which might produce artifacts. 45: You might want to consider using PME electrostatics. 45: 45: 45: 45: There were 2 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 45: 45: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank. 45: Changing nstlist from 10 to 25, rlist from 1.054 to 1.164 45: 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1' 45: 10 steps, 0.0 ps. 45: turning H bonds into constraints... 45: turning H bonds into constraints... 45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 45: Calculated rlist for 1x1 atom pair-list as 1.073 nm, buffer size 0.073 nm 45: Set rlist, assuming 4x4 atom pair-list, to 1.054 nm, buffer size 0.054 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: This run will generate roughly 0 Mb of data 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.017 0.008 197.1 45: (ns/day) (hour/ns) 45: Performance: 226.602 0.106 45: [ OK ] OriresTest.OriresCanRun (337 ms) 45: [----------] 1 test from OriresTest (337 ms total) 45: 45: [----------] 3 tests from PmeTest 45: [ RUN ] PmeTest.ReproducesEnergies 45: Setting the LD random seed to -2065707205 45: Generated 8 of the 10 non-bonded parameter combinations 45: Excluding 2 bonded neighbours molecule type 'Methanol' 45: Excluding 2 bonded neighbours molecule type 'SOL' 45: Number of degrees of freedom in T-Coupling group rest is 12.00 45: 45: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]: 45: NVE simulation: will use the initial temperature of 1046.791 K for 45: determining the Verlet buffer size 45: 45: Estimate for the relative computational load of the PME mesh part: 1.00 45: 45: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]: 45: The optimal PME mesh load for parallel simulations is below 0.5 45: and for highly parallel simulations between 0.25 and 0.33, 45: for higher performance, increase the cut-off and the PME grid spacing. 45: 45: 45: 45: There were 2 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc-and-methanol' 45: 20 steps, 0.0 ps. 45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 45: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 45: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: Calculating fourier grid dimensions for X Y Z 45: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 45: This run will generate roughly 0 Mb of data 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.104 0.052 199.6 45: (ns/day) (hour/ns) 45: Performance: 34.724 0.691 45: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as single precision energy file 45: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc-and-methanol' 45: 20 steps, 0.0 ps. 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.025 0.013 199.0 45: (ns/day) (hour/ns) 45: Performance: 142.804 0.168 45: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as single precision energy file 45: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc-and-methanol' 45: 20 steps, 0.0 ps. 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.036 0.018 199.0 45: (ns/day) (hour/ns) 45: Performance: 101.327 0.237 45: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as single precision energy file 45: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (370 ms) 45: [ RUN ] PmeTest.ScalesTheBox 45: 45: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 45: For a correct single-point energy evaluation with nsteps = 0, use 45: continuation = yes to avoid constraining the input coordinates. 45: 45: Setting the LD random seed to -579010938 45: Generated 8 of the 10 non-bonded parameter combinations 45: Excluding 2 bonded neighbours molecule type 'Methanol' 45: Excluding 2 bonded neighbours molecule type 'SOL' 45: Number of degrees of freedom in T-Coupling group rest is 12.00 45: 45: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 45: NVE simulation: will use the initial temperature of 1046.791 K for 45: determining the Verlet buffer size 45: 45: Estimate for the relative computational load of the PME mesh part: 1.00 45: 45: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 45: The optimal PME mesh load for parallel simulations is below 0.5 45: and for highly parallel simulations between 0.25 and 0.33, 45: for higher performance, increase the cut-off and the PME grid spacing. 45: 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc-and-methanol' 45: 0 steps, 0.0 ps. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.001 0.001 185.6 45: (ns/day) (hour/ns) 45: Performance: 120.036 0.200 45: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as single precision energy file 45: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 45: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 45: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: Calculating fourier grid dimensions for X Y Z 45: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 45: This run will generate roughly 0 Mb of data 45: [ OK ] PmeTest.ScalesTheBox (13 ms) 45: [ RUN ] PmeTest.ScalesTheBoxWithWalls 45: 45: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]: 45: For a correct single-point energy evaluation with nsteps = 0, use 45: continuation = yes to avoid constraining the input coordinates. 45: 45: Setting the LD random seed to -553933825 45: Generated 8 of the 10 non-bonded parameter combinations 45: Excluding 2 bonded neighbours molecule type 'Methanol' 45: Excluding 2 bonded neighbours molecule type 'SOL' 45: Searching the wall atom type(s) 45: Number of degrees of freedom in T-Coupling group rest is 13.00 45: 45: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]: 45: NVE simulation: will use the initial temperature of 966.268 K for 45: determining the Verlet buffer size 45: 45: Estimate for the relative computational load of the PME mesh part: 1.00 45: 45: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]: 45: The optimal PME mesh load for parallel simulations is below 0.5 45: and for highly parallel simulations between 0.25 and 0.33, 45: for higher performance, increase the cut-off and the PME grid spacing. 45: 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc-and-methanol' 45: 0 steps, 0.0 ps. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.011 0.006 195.0 45: (ns/day) (hour/ns) 45: Performance: 14.675 1.635 45: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as single precision energy file 45: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 45: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 45: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: Calculating fourier grid dimensions for X Y Z 45: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 45: This run will generate roughly 0 Mb of data 45: [ OK ] PmeTest.ScalesTheBoxWithWalls (1014 ms) 45: [----------] 3 tests from PmeTest (1397 ms total) 45: 45: [----------] 1 test from CompelTest 45: [ RUN ] CompelTest.SwapCanRun 45: 45: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 45: The Berendsen thermostat does not generate the correct kinetic energy 45: distribution. You might want to consider using the V-rescale thermostat. 45: 45: Setting the LD random seed to 1409101303 45: Generated 330891 of the 330891 non-bonded parameter combinations 45: Generating 1-4 interactions: fudge = 0.5 45: Generated 330891 of the 330891 1-4 parameter combinations 45: Excluding 3 bonded neighbours molecule type 'Protein' 45: Excluding 3 bonded neighbours molecule type 'OCT' 45: Excluding 1 bonded neighbours molecule type 'NA' 45: Excluding 1 bonded neighbours molecule type 'CL' 45: Excluding 3 bonded neighbours molecule type 'Protein' 45: Excluding 3 bonded neighbours molecule type 'OCT' 45: Excluding 2 bonded neighbours molecule type 'SOL' 45: Split0 group 'Ch0' contains 83 atoms. 45: Split1 group 'Ch1' contains 83 atoms. 45: Solvent group 'SOL' contains 11931 atoms. 45: Swap group 'NA+' contains 19 atoms. 45: Swap group 'CL-' contains 19 atoms. 45: Number of degrees of freedom in T-Coupling group System is 27869.00 45: 45: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 45: Removing center of mass motion in the presence of position restraints 45: might cause artifacts. When you are using position restraints to 45: equilibrate a macro-molecule, the artifacts are usually negligible. 45: 45: 45: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 45: You are using a plain Coulomb cut-off, which might produce artifacts. 45: You might want to consider using PME electrostatics. 45: 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: SWAP: Determining initial numbers of ions per compartment. 45: SWAP: Setting pointers for checkpoint writing 45: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 45: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 45: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 45: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 45: starting mdrun 'Channel_coco in octane membrane' 45: 2 steps, 0.0 ps. 45: turning all bonds into constraints... 45: turning all bonds into constraints... 45: turning all bonds into constraints... 45: turning all bonds into constraints... 45: turning all bonds into constraints... 45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 45: Calculated rlist for 1x1 atom pair-list as 1.314 nm, buffer size 0.314 nm 45: Set rlist, assuming 4x4 atom pair-list, to 1.260 nm, buffer size 0.260 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: This run will generate roughly 1 Mb of data 45: 45: Writing final coordinates. 45: 45: NOTE: 45 % of the run time was spent in pair search, 45: you might want to increase nstlist (this has no effect on accuracy) 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.856 0.428 199.9 45: (ns/day) (hour/ns) 45: Performance: 3.026 7.931 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 45: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: SWAP: Setting pointers for checkpoint writing 45: SWAP: Copying channel fluxes from checkpoint file data 45: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 45: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 45: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 45: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 45: starting mdrun 'Channel_coco in octane membrane' 45: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 45: 45: Writing final coordinates. 45: 45: NOTE: 21 % of the run time was spent in pair search, 45: you might want to increase nstlist (this has no effect on accuracy) 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.597 0.299 199.9 45: (ns/day) (hour/ns) 45: Performance: 4.338 5.533 45: [ OK ] CompelTest.SwapCanRun (1807 ms) 45: [----------] 1 test from CompelTest (1807 ms total) 45: 45: [----------] 6 tests from BondedInteractionsTest 45: [ RUN ] BondedInteractionsTest.NormalBondWorks 45: 45: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 45: For a correct single-point energy evaluation with nsteps = 0, use 45: continuation = yes to avoid constraining the input coordinates. 45: 45: Setting the LD random seed to -2230349 45: Generated 3 of the 3 non-bonded parameter combinations 45: Excluding 3 bonded neighbours molecule type 'butane' 45: 45: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 45: In moleculetype 'butane' 2 atoms are not bound by a potential or 45: constraint to any other atom in the same moleculetype. Although 45: technically this might not cause issues in a simulation, this often means 45: that the user forgot to add a bond/potential/constraint or put multiple 45: molecules in the same moleculetype definition by mistake. Run with -v to 45: get information for each atom. 45: 45: Number of degrees of freedom in T-Coupling group rest is 9.00 45: 45: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 45: NVE simulation with an initial temperature of zero: will use a Verlet 45: buffer of 10%. Check your energy drift! 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/butane1.gro' 45: 45: Reading frames from gro file 'A single butane', 4 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: 45: NOTE: 19 % of the run time was spent in pair search, 45: you might want to increase nstlist (this has no effect on accuracy) 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.001 0.000 187.4 45: (ns/day) (hour/ns) 45: Performance: 289.216 0.083 45: This run will generate roughly 0 Mb of data 45: [ OK ] BondedInteractionsTest.NormalBondWorks (6 ms) 45: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 45: 45: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 45: For a correct single-point energy evaluation with nsteps = 0, use 45: continuation = yes to avoid constraining the input coordinates. 45: 45: Setting the LD random seed to 1844440279 45: Generated 3 of the 3 non-bonded parameter combinations 45: Excluding 3 bonded neighbours molecule type 'butane' 45: 45: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 45: In moleculetype 'butane' 2 atoms are not bound by a potential or 45: constraint to any other atom in the same moleculetype. Although 45: technically this might not cause issues in a simulation, this often means 45: that the user forgot to add a bond/potential/constraint or put multiple 45: molecules in the same moleculetype definition by mistake. Run with -v to 45: get information for each atom. 45: 45: Number of degrees of freedom in T-Coupling group rest is 9.00 45: 45: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 45: NVE simulation with an initial temperature of zero: will use a Verlet 45: buffer of 10%. Check your energy drift! 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/butane1.gro' 45: 45: Reading frames from gro file 'A single butane', 4 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: 45: NOTE: 14 % of the run time was spent in pair search, 45: you might want to increase nstlist (this has no effect on accuracy) 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.000 0.000 185.9 45: (ns/day) (hour/ns) 45: Performance: 330.646 0.073 45: This run will generate roughly 0 Mb of data 45: [ OK ] BondedInteractionsTest.TabulatedBondWorks (6 ms) 45: [ RUN ] BondedInteractionsTest.NormalAngleWorks 45: 45: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 45: For a correct single-point energy evaluation with nsteps = 0, use 45: continuation = yes to avoid constraining the input coordinates. 45: 45: Setting the LD random seed to -94910481 45: Generated 3 of the 3 non-bonded parameter combinations 45: Excluding 3 bonded neighbours molecule type 'butane' 45: 45: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 45: In moleculetype 'butane' 4 atoms are not bound by a potential or 45: constraint to any other atom in the same moleculetype. Although 45: technically this might not cause issues in a simulation, this often means 45: that the user forgot to add a bond/potential/constraint or put multiple 45: molecules in the same moleculetype definition by mistake. Run with -v to 45: get information for each atom. 45: 45: Number of degrees of freedom in T-Coupling group rest is 9.00 45: 45: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 45: NVE simulation with an initial temperature of zero: will use a Verlet 45: buffer of 10%. Check your energy drift! 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/butane1.gro' 45: 45: Reading frames from gro file 'A single butane', 4 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: 45: NOTE: 13 % of the run time was spent in pair search, 45: you might want to increase nstlist (this has no effect on accuracy) 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.001 0.001 188.9 45: (ns/day) (hour/ns) 45: Performance: 131.063 0.183 45: This run will generate roughly 0 Mb of data 45: [ OK ] BondedInteractionsTest.NormalAngleWorks (36 ms) 45: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 45: 45: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 45: For a correct single-point energy evaluation with nsteps = 0, use 45: continuation = yes to avoid constraining the input coordinates. 45: 45: Setting the LD random seed to 1559977983 45: Generated 3 of the 3 non-bonded parameter combinations 45: Excluding 3 bonded neighbours molecule type 'butane' 45: 45: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 45: In moleculetype 'butane' 4 atoms are not bound by a potential or 45: constraint to any other atom in the same moleculetype. Although 45: technically this might not cause issues in a simulation, this often means 45: that the user forgot to add a bond/potential/constraint or put multiple 45: molecules in the same moleculetype definition by mistake. Run with -v to 45: get information for each atom. 45: 45: Number of degrees of freedom in T-Coupling group rest is 9.00 45: 45: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 45: NVE simulation with an initial temperature of zero: will use a Verlet 45: buffer of 10%. Check your energy drift! 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/butane1.gro' 45: 45: Reading frames from gro file 'A single butane', 4 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: 45: NOTE: 13 % of the run time was spent in pair search, 45: you might want to increase nstlist (this has no effect on accuracy) 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.001 0.000 187.8 45: (ns/day) (hour/ns) 45: Performance: 219.230 0.109 45: This run will generate roughly 0 Mb of data 45: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (9 ms) 45: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 45: 45: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 45: For a correct single-point energy evaluation with nsteps = 0, use 45: continuation = yes to avoid constraining the input coordinates. 45: 45: Setting the LD random seed to -1352122370 45: Generated 3 of the 3 non-bonded parameter combinations 45: Excluding 3 bonded neighbours molecule type 'butane' 45: 45: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 45: In moleculetype 'butane' 4 atoms are not bound by a potential or 45: constraint to any other atom in the same moleculetype. Although 45: technically this might not cause issues in a simulation, this often means 45: that the user forgot to add a bond/potential/constraint or put multiple 45: molecules in the same moleculetype definition by mistake. Run with -v to 45: get information for each atom. 45: 45: Number of degrees of freedom in T-Coupling group rest is 9.00 45: 45: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 45: NVE simulation with an initial temperature of zero: will use a Verlet 45: buffer of 10%. Check your energy drift! 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/butane1.gro' 45: 45: Reading frames from gro file 'A single butane', 4 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: 45: NOTE: 13 % of the run time was spent in pair search, 45: you might want to increase nstlist (this has no effect on accuracy) 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.001 0.000 188.3 45: (ns/day) (hour/ns) 45: Performance: 211.305 0.114 45: This run will generate roughly 0 Mb of data 45: [ OK ] BondedInteractionsTest.NormalDihedralWorks (8 ms) 45: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 45: 45: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 45: For a correct single-point energy evaluation with nsteps = 0, use 45: continuation = yes to avoid constraining the input coordinates. 45: 45: Setting the LD random seed to -8709445 45: Generated 3 of the 3 non-bonded parameter combinations 45: Excluding 3 bonded neighbours molecule type 'butane' 45: 45: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 45: In moleculetype 'butane' 4 atoms are not bound by a potential or 45: constraint to any other atom in the same moleculetype. Although 45: technically this might not cause issues in a simulation, this often means 45: that the user forgot to add a bond/potential/constraint or put multiple 45: molecules in the same moleculetype definition by mistake. Run with -v to 45: get information for each atom. 45: 45: Number of degrees of freedom in T-Coupling group rest is 9.00 45: 45: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 45: NVE simulation with an initial temperature of zero: will use a Verlet 45: buffer of 10%. Check your energy drift! 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/butane1.gro' 45: 45: Reading frames from gro file 'A single butane', 4 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: 45: NOTE: 11 % of the run time was spent in pair search, 45: you might want to increase nstlist (this has no effect on accuracy) 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.001 0.000 187.3 45: (ns/day) (hour/ns) 45: Performance: 220.968 0.109 45: This run will generate roughly 0 Mb of data 45: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (11 ms) 45: [----------] 6 tests from BondedInteractionsTest (77 ms total) 45: 45: [----------] Global test environment tear-down 45: [==========] 12 tests from 5 test cases ran. (3790 ms total) 45: [ PASSED ] 12 tests. 45: 45: YOU HAVE 12 DISABLED TESTS 45: 45/54 Test #45: MdrunTests .......................... Passed 3.81 sec test 46 Start 46: MdrunNonIntegratorTests 46: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/MdrunNonIntegratorTests.xml" 46: Test timeout computed to be: 600 46: [==========] Running 58 tests from 5 test cases. 46: [----------] Global test environment set-up. 46: [----------] 1 test from NonbondedBenchTest 46: [ RUN ] NonbondedBenchTest.BasicEndToEndTest 46: SIMD width: 4 46: System size: 3000 atoms 46: Cut-off radius: 1 nm 46: Number of threads: 1 46: Number of iterations: 1 46: Compute energies: no 46: Ewald excl. corr.: analytical 46: 46: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle 46: total useful 46: Ewald all geom. 4xM 20.021 20.0205 0.0595 0.0315 46: [ OK ] NonbondedBenchTest.BasicEndToEndTest (26 ms) 46: [----------] 1 test from NonbondedBenchTest (26 ms total) 46: 46: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 330891 of the 330891 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 330891 of the 330891 1-4 parameter combinations 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 27.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Steepest Descents: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: 46: Energy minimization reached the maximum number of steps before the forces 46: reached the requested precision Fmax < 10. 46: 46: writing lowest energy coordinates. 46: 46: Steepest Descents did not converge to Fmax < 10 in 5 steps. 46: Potential Energy = -4.7990963e+01 46: Maximum force = 1.8629691e+02 on atom 13 46: Norm of force = 8.7721773e+01 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (595 ms) 46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 330891 of the 330891 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 330891 of the 330891 1-4 parameter combinations 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 27.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Polak-Ribiere Conjugate Gradients: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: F-max = 3.02331e+02 on atom 3 46: F-Norm = 1.18024e+02 46: 46: 46: Energy minimization reached the maximum number of steps before the forces 46: reached the requested precision Fmax < 10. 46: 46: writing lowest energy coordinates. 46: 46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 46: Potential Energy = -5.5862499e+01 46: Maximum force = 4.2727313e+02 on atom 13 46: Norm of force = 1.8452925e+02 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (513 ms) 46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 20503 of the 20503 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 1 46: Generated 17396 of the 20503 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Glycine' 46: Number of degrees of freedom in T-Coupling group System is 22.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Steepest Descents: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: 46: Energy minimization reached the maximum number of steps before the forces 46: reached the requested precision Fmax < 10. 46: 46: writing lowest energy coordinates. 46: 46: Steepest Descents did not converge to Fmax < 10 in 5 steps. 46: Potential Energy = 3.1937723e+02 46: Maximum force = 9.9988623e+03 on atom 9 46: Norm of force = 4.6166987e+03 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 turning H bonds into constraints... 46: This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (266 ms) 46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 20503 of the 20503 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 1 46: Generated 17396 of the 20503 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Glycine' 46: 46: NOTE 3 [file glycine_vacuo.top, line 12]: 46: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 46: 46: Number of degrees of freedom in T-Coupling group System is 22.00 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Polak-Ribiere Conjugate Gradients: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: F-max = 2.41575e+04 on atom 10 46: F-Norm = 1.18451e+04 46: 46: 46: Energy minimization reached the maximum number of steps before the forces 46: reached the requested precision Fmax < 10. 46: 46: writing lowest energy coordinates. 46: 46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 46: Potential Energy = 1.5174380e+02 46: Maximum force = 7.4208838e+03 on atom 9 46: Norm of force = 3.5693002e+03 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 turning H bonds into constraints... 46: This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (219 ms) 46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 2145 of the 2145 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2145 of the 2145 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 46: 46: NOTE 3 [file unknown]: 46: You are using constraints on all bonds, whereas the forcefield has been 46: parametrized only with constraints involving hydrogen atoms. We suggest 46: using constraints = h-bonds instead, this will also improve performance. 46: 46: Cleaning up constraints and constant bonded interactions with virtual sites 46: Removed 18 Angles with virtual sites, 21 left 46: Removed 10 Proper Dih.s with virtual sites, 44 left 46: Converted 15 Constraints with virtual sites to connections, 7 left 46: Number of degrees of freedom in T-Coupling group System is 23.00 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Steepest Descents: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: 46: Energy minimization reached the maximum number of steps before the forces 46: reached the requested precision Fmax < 10. 46: 46: writing lowest energy coordinates. 46: 46: Steepest Descents did not converge to Fmax < 10 in 5 steps. 46: Potential Energy = -1.5698450e+02 46: Maximum force = 4.5703430e+02 on atom 17 46: Norm of force = 1.8327605e+02 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 turning all bonds into constraints... 46: This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (23 ms) 46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 2145 of the 2145 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2145 of the 2145 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 46: 46: NOTE 3 [file unknown]: 46: You are using constraints on all bonds, whereas the forcefield has been 46: parametrized only with constraints involving hydrogen atoms. We suggest 46: using constraints = h-bonds instead, this will also improve performance. 46: 46: 46: NOTE 4 [file unknown]: 46: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 46: 46: Cleaning up constraints and constant bonded interactions with virtual sites 46: Removed 18 Angles with virtual sites, 21 left 46: Removed 10 Proper Dih.s with virtual sites, 44 left 46: Converted 15 Constraints with virtual sites to connections, 7 left 46: Number of degrees of freedom in T-Coupling group System is 23.00 46: 46: NOTE 5 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 5 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Polak-Ribiere Conjugate Gradients: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: F-max = 1.06799e+03 on atom 28 46: F-Norm = 4.26916e+02 46: 46: 46: Energy minimization reached the maximum number of steps before the forces 46: reached the requested precision Fmax < 10. 46: 46: writing lowest energy coordinates. 46: 46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 46: Potential Energy = -1.6941095e+02 46: Maximum force = 2.1833020e+02 on atom 17 46: Norm of force = 7.9215281e+01 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 turning all bonds into constraints... 46: This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (51 ms) 46: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (1668 ms total) 46: 46: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 1 of the 1 non-bonded parameter combinations 46: Excluding 1 bonded neighbours molecule type 'Argon' 46: Number of degrees of freedom in T-Coupling group System is 33.00 46: 46: There were 2 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Steepest Descents: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: 46: writing lowest energy coordinates. 46: 46: Steepest Descents converged to Fmax < 10 in 1 steps 46: Potential Energy = -9.7425687e-01 46: Maximum force = 4.0132279e+00 on atom 1 46: Norm of force = 1.6383933e+00 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (13 ms) 46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 1 of the 1 non-bonded parameter combinations 46: Excluding 1 bonded neighbours molecule type 'Argon' 46: Number of degrees of freedom in T-Coupling group System is 33.00 46: 46: There were 2 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Polak-Ribiere Conjugate Gradients: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: F-max = 4.01323e+00 on atom 1 46: F-Norm = 1.63839e+00 46: 46: 46: writing lowest energy coordinates. 46: 46: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 46: Potential Energy = -9.9064195e-01 46: Maximum force = 2.5781672e+00 on atom 1 46: Norm of force = 1.0525324e+00 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (8 ms) 46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: 46: WARNING 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 46: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 46: 46: Generated 1 of the 1 non-bonded parameter combinations 46: Excluding 1 bonded neighbours molecule type 'Argon' 46: Number of degrees of freedom in T-Coupling group System is 33.00 46: 46: There were 2 notes 46: 46: There was 1 warning 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: 46: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Low-Memory BFGS Minimizer: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: Using 10 BFGS correction steps. 46: 46: F-max = 4.01323e+00 on atom 1 46: F-Norm = 1.63839e+00 46: 46: 46: writing lowest energy coordinates. 46: 46: Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps 46: Potential Energy = -9.9064195e-01 46: Maximum force = 2.5781672e+00 on atom 1 46: Norm of force = 1.0525324e+00 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (9 ms) 46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 20503 of the 20503 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 1 46: Generated 17396 of the 20503 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Glycine' 46: Number of degrees of freedom in T-Coupling group System is 27.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Steepest Descents: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: 46: Energy minimization reached the maximum number of steps before the forces 46: reached the requested precision Fmax < 10. 46: 46: writing lowest energy coordinates. 46: 46: Steepest Descents did not converge to Fmax < 10 in 5 steps. 46: Potential Energy = 3.1939700e+02 46: Maximum force = 9.9704248e+03 on atom 9 46: Norm of force = 4.6227540e+03 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (236 ms) 46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 20503 of the 20503 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 1 46: Generated 17396 of the 20503 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Glycine' 46: Number of degrees of freedom in T-Coupling group System is 27.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Polak-Ribiere Conjugate Gradients: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: F-max = 2.41672e+04 on atom 10 46: F-Norm = 1.19357e+04 46: 46: 46: Energy minimization reached the maximum number of steps before the forces 46: reached the requested precision Fmax < 10. 46: 46: writing lowest energy coordinates. 46: 46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 46: Potential Energy = 1.5625763e+02 46: Maximum force = 7.5018252e+03 on atom 9 46: Norm of force = 3.6139025e+03 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (189 ms) 46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: 46: WARNING 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 46: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 46: 46: Generated 20503 of the 20503 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 1 46: Generated 17396 of the 20503 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Glycine' 46: Number of degrees of freedom in T-Coupling group System is 27.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: 46: There was 1 warning 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: 46: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Low-Memory BFGS Minimizer: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: Using 10 BFGS correction steps. 46: 46: F-max = 2.41672e+04 on atom 10 46: F-Norm = 1.19357e+04 46: 46: 46: Energy minimization reached the maximum number of steps before the forces 46: reached the requested precision Fmax < 10. 46: 46: writing lowest energy coordinates. 46: 46: Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps. 46: Potential Energy = 5.6111725e+02 46: Maximum force = 1.2685491e+04 on atom 10 46: Norm of force = 6.0643622e+03 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (165 ms) 46: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (620 ms total) 46: 46: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 1 of the 1 non-bonded parameter combinations 46: Excluding 1 bonded neighbours molecule type 'Argon' 46: Number of degrees of freedom in T-Coupling group System is 33.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 46: NVE simulation: will use the initial temperature of 68.810 K for 46: determining the Verlet buffer size 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'Argon' 46: 16 steps, 0.0 ps. 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 46: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.007 0.003 197.7 46: (ns/day) (hour/ns) 46: Performance: 420.404 0.057 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'Argon', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr' 46: 46: trr version: GMX_trn_file (single precision) 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 16 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.001 0.001 193.8 46: (ns/day) (hour/ns) 46: Performance: 2786.338 0.009 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (12 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 1 of the 1 non-bonded parameter combinations 46: Excluding 1 bonded neighbours molecule type 'Argon' 46: Number of degrees of freedom in T-Coupling group System is 33.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 46: NVE simulation: will use the initial temperature of 68.810 K for 46: determining the Verlet buffer size 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'Argon' 46: 16 steps, 0.0 ps. 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 46: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.304 0.152 199.9 46: (ns/day) (hour/ns) 46: Performance: 9.647 2.488 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'Argon', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 13 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.002 0.001 193.4 46: (ns/day) (hour/ns) 46: Performance: 1431.697 0.017 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (165 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 1 of the 1 non-bonded parameter combinations 46: Excluding 1 bonded neighbours molecule type 'Argon' 46: Number of degrees of freedom in T-Coupling group System is 33.00 46: 46: There were 2 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'Argon' 46: 16 steps, 0.0 ps. 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 46: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.011 0.006 197.3 46: (ns/day) (hour/ns) 46: Performance: 266.093 0.090 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'Argon', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 12 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.002 0.001 195.7 46: (ns/day) (hour/ns) 46: Performance: 1704.647 0.014 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (18 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 1 of the 1 non-bonded parameter combinations 46: Excluding 1 bonded neighbours molecule type 'Argon' 46: Number of degrees of freedom in T-Coupling group System is 33.00 46: 46: There were 2 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'Argon' 46: 16 steps, 0.0 ps. 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 46: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.006 0.003 195.8 46: (ns/day) (hour/ns) 46: Performance: 515.401 0.047 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'Argon', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 15 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.001 0.001 194.6 46: (ns/day) (hour/ns) 46: Performance: 2039.256 0.012 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (14 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 330891 of the 330891 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 330891 of the 330891 1-4 parameter combinations 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 27.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 46: NVE simulation: will use the initial temperature of 398.997 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'spc2' 46: 16 steps, 0.0 ps. 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 46: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.013 0.007 197.4 46: (ns/day) (hour/ns) 46: Performance: 225.357 0.106 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'spc2', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 16 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.002 0.001 194.0 46: (ns/day) (hour/ns) 46: Performance: 1763.697 0.014 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (587 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 330891 of the 330891 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 330891 of the 330891 1-4 parameter combinations 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 27.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 46: NVE simulation: will use the initial temperature of 398.997 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'spc2' 46: 16 steps, 0.0 ps. 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 46: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.046 0.023 199.7 46: (ns/day) (hour/ns) 46: Performance: 63.730 0.377 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'spc2', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.004 0.002 197.3 46: (ns/day) (hour/ns) 46: Performance: 759.910 0.032 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (588 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 330891 of the 330891 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 330891 of the 330891 1-4 parameter combinations 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 27.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'spc2' 46: 16 steps, 0.0 ps. 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.735 nm, buffer size 0.035 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.733 nm, buffer size 0.033 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.007 0.004 194.4 46: (ns/day) (hour/ns) 46: Performance: 410.788 0.058 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'spc2', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 18 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.002 0.001 194.1 46: (ns/day) (hour/ns) 46: Performance: 1305.764 0.018 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (596 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 330891 of the 330891 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 330891 of the 330891 1-4 parameter combinations 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 27.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'spc2' 46: 16 steps, 0.0 ps. 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.010 0.005 197.1 46: (ns/day) (hour/ns) 46: Performance: 296.896 0.081 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'spc2', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 20 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.002 0.001 193.3 46: (ns/day) (hour/ns) 46: Performance: 1518.510 0.016 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (617 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2145 of the 2145 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2145 of the 2145 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 46: 46: NOTE 3 [file unknown]: 46: You are using constraints on all bonds, whereas the forcefield has been 46: parametrized only with constraints involving hydrogen atoms. We suggest 46: using constraints = h-bonds instead, this will also improve performance. 46: 46: Cleaning up constraints and constant bonded interactions with virtual sites 46: Removed 18 Angles with virtual sites, 21 left 46: Removed 10 Proper Dih.s with virtual sites, 44 left 46: Converted 15 Constraints with virtual sites to connections, 7 left 46: Number of degrees of freedom in T-Coupling group System is 23.00 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 46: NVE simulation: will use the initial temperature of 456.887 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 5 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 46: There are 9 non-linear virtual site constructions. Their contribution to 46: the energy error is approximated. In most cases this does not affect the 46: error significantly. 46: 46: 46: NOTE 6 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 6 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'Alanine dipeptide in vacuo' 46: 16 steps, 0.0 ps. 46: turning all bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 46: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.025 0.013 198.6 46: (ns/day) (hour/ns) 46: Performance: 117.142 0.205 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.026 0.013 199.4 46: (ns/day) (hour/ns) 46: Performance: 113.866 0.211 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (57 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2145 of the 2145 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2145 of the 2145 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 46: 46: NOTE 3 [file unknown]: 46: You are using constraints on all bonds, whereas the forcefield has been 46: parametrized only with constraints involving hydrogen atoms. We suggest 46: using constraints = h-bonds instead, this will also improve performance. 46: 46: Cleaning up constraints and constant bonded interactions with virtual sites 46: Removed 18 Angles with virtual sites, 21 left 46: Removed 10 Proper Dih.s with virtual sites, 44 left 46: Converted 15 Constraints with virtual sites to connections, 7 left 46: Number of degrees of freedom in T-Coupling group System is 23.00 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 46: NVE simulation: will use the initial temperature of 456.887 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 5 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 46: There are 9 non-linear virtual site constructions. Their contribution to 46: the energy error is approximated. In most cases this does not affect the 46: error significantly. 46: 46: 46: NOTE 6 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 6 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'Alanine dipeptide in vacuo' 46: 16 steps, 0.0 ps. 46: turning all bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 46: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.046 0.023 199.3 46: (ns/day) (hour/ns) 46: Performance: 63.287 0.379 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 18 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.002 0.001 195.7 46: (ns/day) (hour/ns) 46: Performance: 1479.489 0.016 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (76 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2145 of the 2145 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2145 of the 2145 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 46: 46: NOTE 3 [file unknown]: 46: You are using constraints on all bonds, whereas the forcefield has been 46: parametrized only with constraints involving hydrogen atoms. We suggest 46: using constraints = h-bonds instead, this will also improve performance. 46: 46: Cleaning up constraints and constant bonded interactions with virtual sites 46: Removed 18 Angles with virtual sites, 21 left 46: Removed 10 Proper Dih.s with virtual sites, 44 left 46: Converted 15 Constraints with virtual sites to connections, 7 left 46: Number of degrees of freedom in T-Coupling group System is 23.00 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 46: There are 9 non-linear virtual site constructions. Their contribution to 46: the energy error is approximated. In most cases this does not affect the 46: error significantly. 46: 46: 46: NOTE 5 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 5 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'Alanine dipeptide in vacuo' 46: 16 steps, 0.0 ps. 46: turning all bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.017 0.008 197.7 46: (ns/day) (hour/ns) 46: Performance: 175.141 0.137 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 15 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.002 0.001 193.6 46: (ns/day) (hour/ns) 46: Performance: 1303.278 0.018 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (81 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2145 of the 2145 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2145 of the 2145 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 46: 46: NOTE 3 [file unknown]: 46: You are using constraints on all bonds, whereas the forcefield has been 46: parametrized only with constraints involving hydrogen atoms. We suggest 46: using constraints = h-bonds instead, this will also improve performance. 46: 46: Cleaning up constraints and constant bonded interactions with virtual sites 46: Removed 18 Angles with virtual sites, 21 left 46: Removed 10 Proper Dih.s with virtual sites, 44 left 46: Converted 15 Constraints with virtual sites to connections, 7 left 46: Number of degrees of freedom in T-Coupling group System is 23.00 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 46: There are 9 non-linear virtual site constructions. Their contribution to 46: the energy error is approximated. In most cases this does not affect the 46: error significantly. 46: 46: 46: NOTE 5 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 5 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'Alanine dipeptide in vacuo' 46: 16 steps, 0.0 ps. 46: turning all bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.087 0.044 198.2 46: (ns/day) (hour/ns) 46: Performance: 33.507 0.716 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 13 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.002 0.001 192.8 46: (ns/day) (hour/ns) 46: Performance: 1162.596 0.021 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (87 ms) 46: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (2898 ms total) 46: 46: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.014 0.007 197.0 46: (ns/day) (hour/ns) 46: Performance: 214.028 0.112 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 12 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 187.7 46: (ns/day) (hour/ns) 46: Performance: 857.782 0.028 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (35 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.013 0.007 196.3 46: (ns/day) (hour/ns) 46: Performance: 217.144 0.111 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 11 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 174.5 46: (ns/day) (hour/ns) 46: Performance: 870.140 0.028 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (76 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.114 0.057 199.6 46: (ns/day) (hour/ns) 46: Performance: 25.679 0.935 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 13 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 181.8 46: (ns/day) (hour/ns) 46: Performance: 1046.119 0.023 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (82 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.010 0.005 195.8 46: (ns/day) (hour/ns) 46: Performance: 291.061 0.082 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 10 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 189.1 46: (ns/day) (hour/ns) 46: Performance: 821.084 0.029 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (34 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.131 0.066 199.4 46: (ns/day) (hour/ns) 46: Performance: 22.368 1.073 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 12 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.002 0.001 187.2 46: (ns/day) (hour/ns) 46: Performance: 1226.233 0.020 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (128 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.008 0.004 196.6 46: (ns/day) (hour/ns) 46: Performance: 375.554 0.064 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 11 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.002 0.001 189.2 46: (ns/day) (hour/ns) 46: Performance: 1290.447 0.019 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (24 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.011 0.006 195.5 46: (ns/day) (hour/ns) 46: Performance: 253.356 0.095 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 11 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 180.5 46: (ns/day) (hour/ns) 46: Performance: 870.632 0.028 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (37 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.014 0.007 197.7 46: (ns/day) (hour/ns) 46: Performance: 207.260 0.116 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 11 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 188.9 46: (ns/day) (hour/ns) 46: Performance: 1108.419 0.022 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (67 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.379 0.190 199.8 46: (ns/day) (hour/ns) 46: Performance: 7.740 3.101 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 12 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 184.1 46: (ns/day) (hour/ns) 46: Performance: 841.611 0.029 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (223 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.008 0.004 192.2 46: (ns/day) (hour/ns) 46: Performance: 340.741 0.070 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 13 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.002 0.001 182.4 46: (ns/day) (hour/ns) 46: Performance: 1212.477 0.020 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (27 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.085 0.042 199.3 46: (ns/day) (hour/ns) 46: Performance: 34.633 0.693 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 11 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 188.8 46: (ns/day) (hour/ns) 46: Performance: 931.870 0.026 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (66 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.014 0.007 198.5 46: (ns/day) (hour/ns) 46: Performance: 215.586 0.111 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 11 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.004 0.002 188.1 46: (ns/day) (hour/ns) 46: Performance: 742.061 0.032 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (39 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.014 0.007 198.5 46: (ns/day) (hour/ns) 46: Performance: 202.711 0.118 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.007 0.004 194.2 46: (ns/day) (hour/ns) 46: Performance: 394.001 0.061 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (77 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.016 0.008 198.7 46: (ns/day) (hour/ns) 46: Performance: 188.127 0.128 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 15 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 185.5 46: (ns/day) (hour/ns) 46: Performance: 986.800 0.024 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (69 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.010 0.005 198.2 46: (ns/day) (hour/ns) 46: Performance: 291.557 0.082 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 15 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 186.1 46: (ns/day) (hour/ns) 46: Performance: 927.521 0.026 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (31 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.009 0.005 198.5 46: (ns/day) (hour/ns) 46: Performance: 309.951 0.077 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.006 0.003 193.0 46: (ns/day) (hour/ns) 46: Performance: 476.863 0.050 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (73 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.012 0.006 198.2 46: (ns/day) (hour/ns) 46: Performance: 242.572 0.099 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 12 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 189.5 46: (ns/day) (hour/ns) 46: Performance: 819.228 0.029 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (36 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.014 0.007 198.6 46: (ns/day) (hour/ns) 46: Performance: 215.428 0.111 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 15 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 187.5 46: (ns/day) (hour/ns) 46: Performance: 977.562 0.025 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (76 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.009 0.005 198.5 46: (ns/day) (hour/ns) 46: Performance: 310.623 0.077 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 15 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.002 0.001 187.7 46: (ns/day) (hour/ns) 46: Performance: 1132.879 0.021 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (26 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.012 0.006 198.6 46: (ns/day) (hour/ns) 46: Performance: 236.955 0.101 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 15 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 188.8 46: (ns/day) (hour/ns) 46: Performance: 1047.720 0.023 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (77 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.012 0.006 198.3 46: (ns/day) (hour/ns) 46: Performance: 235.749 0.102 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 15 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 185.7 46: (ns/day) (hour/ns) 46: Performance: 1038.361 0.023 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (29 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.013 0.007 198.3 46: (ns/day) (hour/ns) 46: Performance: 221.357 0.108 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 13 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 184.8 46: (ns/day) (hour/ns) 46: Performance: 835.221 0.029 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (82 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.095 0.048 199.5 46: (ns/day) (hour/ns) 46: Performance: 30.751 0.780 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 16 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 188.1 46: (ns/day) (hour/ns) 46: Performance: 1083.848 0.022 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (85 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.012 0.006 196.8 46: (ns/day) (hour/ns) 46: Performance: 232.037 0.103 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 11 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.005 0.002 188.0 46: (ns/day) (hour/ns) 46: Performance: 602.503 0.040 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (94 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.011 0.006 195.1 46: (ns/day) (hour/ns) 46: Performance: 258.371 0.093 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.087 0.044 198.8 46: (ns/day) (hour/ns) 46: Performance: 33.410 0.718 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (95 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.025 0.013 195.7 46: (ns/day) (hour/ns) 46: Performance: 117.013 0.205 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 15 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 187.9 46: (ns/day) (hour/ns) 46: Performance: 1087.483 0.022 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (105 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.727 0.364 199.9 46: (ns/day) (hour/ns) 46: Performance: 4.038 5.943 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 12 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 188.2 46: (ns/day) (hour/ns) 46: Performance: 968.190 0.025 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (415 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.109 0.055 199.5 46: (ns/day) (hour/ns) 46: Performance: 26.802 0.895 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 13 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 186.7 46: (ns/day) (hour/ns) 46: Performance: 856.471 0.028 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (92 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.014 0.007 195.4 46: (ns/day) (hour/ns) 46: Performance: 203.219 0.118 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 12 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.005 0.003 187.2 46: (ns/day) (hour/ns) 46: Performance: 580.257 0.041 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (97 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.013 0.007 196.3 46: (ns/day) (hour/ns) 46: Performance: 222.059 0.108 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 11 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 188.1 46: (ns/day) (hour/ns) 46: Performance: 871.988 0.028 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (98 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.012 0.006 196.0 46: (ns/day) (hour/ns) 46: Performance: 240.067 0.100 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 12 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.005 0.003 188.2 46: (ns/day) (hour/ns) 46: Performance: 579.221 0.041 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (104 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.013 0.007 196.5 46: (ns/day) (hour/ns) 46: Performance: 218.577 0.110 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 13 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 187.9 46: (ns/day) (hour/ns) 46: Performance: 1012.257 0.024 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (105 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.012 0.006 196.3 46: (ns/day) (hour/ns) 46: Performance: 250.390 0.096 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 15 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 185.4 46: (ns/day) (hour/ns) 46: Performance: 1075.898 0.022 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as single precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as single precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (90 ms) 46: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (2795 ms total) 46: 46: [----------] Global test environment tear-down 46: [==========] 58 tests from 5 test cases ran. (8007 ms total) 46: [ PASSED ] 58 tests. 46/54 Test #46: MdrunNonIntegratorTests ............. Passed 8.08 sec test 47 Start 47: MdrunTpiTests 47: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/mdrun-tpi-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/MdrunTpiTests.xml" 47: Test timeout computed to be: 600 47: [==========] Running 2 tests from 1 test case. 47: [----------] Global test environment set-up. 47: [----------] 2 tests from Simple/TpiTest 47: [ RUN ] Simple/TpiTest.ReproducesOutput/0 47: Ignoring obsolete mdp entry 'ns_type' 47: Generated 331705 of the 331705 non-bonded parameter combinations 47: Generating 1-4 interactions: fudge = 0.5 47: Generated 331705 of the 331705 1-4 parameter combinations 47: Excluding 2 bonded neighbours molecule type 'SOL' 47: Excluding 3 bonded neighbours molecule type 'methane' 47: Number of degrees of freedom in T-Coupling group System is 1308.00 47: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 47: log). 47: The current CPU can measure timings more accurately than the code in 47: mdrun-tpi-test was configured to use. This might affect your simulation 47: speed as accurate timings are needed for load-balancing. 47: Please consider rebuilding mdrun-tpi-test with the GMX_USE_RDTSCP=ON CMake option. 47: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 47: 47: TPI is not implemented for GPUs. 47: 47: Using 1 MPI thread 47: 47: Non-default thread affinity set, disabling internal thread affinity 47: 47: Using 1 OpenMP thread 47: 47: Reading frames from gro file '216 water molecules', 648 atoms. 47: Reading frame 0 time 0.000 mu 8.706e+02 8.706e+02 47: Last frame 0 time 0.000 47: Analysing residue names: 47: There are: 216 Water residues 47: There are: 1 Other residues 47: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 47: This run will generate roughly 0 Mb of data 47: [ OK ] Simple/TpiTest.ReproducesOutput/0 (590 ms) 47: [ RUN ] Simple/TpiTest.ReproducesOutput/1 47: Ignoring obsolete mdp entry 'ns_type' 47: Generated 331705 of the 331705 non-bonded parameter combinations 47: Generating 1-4 interactions: fudge = 0.5 47: Generated 331705 of the 331705 1-4 parameter combinations 47: Excluding 2 bonded neighbours molecule type 'SOL' 47: Excluding 3 bonded neighbours molecule type 'methane' 47: Number of degrees of freedom in T-Coupling group System is 1308.00 47: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 47: log). 47: The current CPU can measure timings more accurately than the code in 47: mdrun-tpi-test was configured to use. This might affect your simulation 47: speed as accurate timings are needed for load-balancing. 47: Please consider rebuilding mdrun-tpi-test with the GMX_USE_RDTSCP=ON CMake option. 47: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 47: 47: TPI is not implemented for GPUs. 47: 47: Using 1 MPI thread 47: 47: Non-default thread affinity set, disabling internal thread affinity 47: 47: Using 1 OpenMP thread 47: 47: Reading frames from gro file '216 water molecules', 648 atoms. 47: Reading frame 0 time 0.000 mu 9.144e+01 9.144e+01 47: Last frame 0 time 0.000 47: Analysing residue names: 47: There are: 216 Water residues 47: There are: 1 Other residues 47: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 47: This run will generate roughly 0 Mb of data 47: [ OK ] Simple/TpiTest.ReproducesOutput/1 (501 ms) 47: [----------] 2 tests from Simple/TpiTest (1091 ms total) 47: 47: [----------] Global test environment tear-down 47: [==========] 2 tests from 1 test case ran. (1091 ms total) 47: [ PASSED ] 2 tests. 47/54 Test #47: MdrunTpiTests ....................... Passed 1.10 sec test 48 Start 48: MdrunMpiTests 48: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/MdrunMpiTests.xml" 48: Test timeout computed to be: 600 48: [==========] Running 22 tests from 7 test cases. 48: [----------] Global test environment set-up. 48: [----------] 1 test from DomainDecompositionSpecialCasesTest 48: [ RUN ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: 48: For a correct single-point energy evaluation with nsteps = 0, use 48: continuation = yes to avoid constraining the input coordinates. 48: 48: Setting the LD random seed to -151257921 48: Generated 3 of the 3 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 0.5 48: Generated 3 of the 3 1-4 parameter combinations 48: Excluding 2 bonded neighbours molecule type 'SOL' 48: Number of degrees of freedom in T-Coupling group rest is 9.00 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: 48: NVE simulation with an initial temperature of zero: will use a Verlet 48: buffer of 10%. Check your energy drift! 48: 48: 48: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting mdrun 'spc2' 48: 0 steps, 0.0 ps. 48: 48: NOTE: 23 % of the run time was spent in domain decomposition, 48: 18 % of the run time was spent in pair search, 48: you might want to increase nstlist (this has no effect on accuracy) 48: 48: Core t (s) Wall t (s) (%) 48: Time: 0.001 0.000 303.6 48: (ns/day) (hour/ns) 48: Performance: 268.435 0.089 48: This run will generate roughly 0 Mb of data 48: [ OK ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks (87 ms) 48: [----------] 1 test from DomainDecompositionSpecialCasesTest (87 ms total) 48: 48: [----------] 4 tests from MimicTest 48: [ RUN ] MimicTest.OneQuantumMol 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 48: For a correct single-point energy evaluation with nsteps = 0, use 48: continuation = yes to avoid constraining the input coordinates. 48: 48: Setting the LD random seed to 1071579103 48: Generated 10 of the 10 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 0.5 48: Generated 10 of the 10 1-4 parameter combinations 48: Excluding 2 bonded neighbours molecule type 'SOL' 48: Number of degrees of freedom in T-Coupling group rest is 21.00 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 48: NVE simulation with an initial temperature of zero: will use a Verlet 48: buffer of 10%. Check your energy drift! 48: 48: 48: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/4water.gro' 48: 48: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: 48: NOTE: 15 % of the run time was spent in domain decomposition, 48: 11 % of the run time was spent in pair search, 48: you might want to increase nstlist (this has no effect on accuracy) 48: 48: Core t (s) Wall t (s) (%) 48: Time: 0.002 0.001 378.2 48: (ns/day) (hour/ns) 48: Performance: 159.396 0.151 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 48: [ OK ] MimicTest.OneQuantumMol (12 ms) 48: [ RUN ] MimicTest.AllQuantumMol 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 48: For a correct single-point energy evaluation with nsteps = 0, use 48: continuation = yes to avoid constraining the input coordinates. 48: 48: Setting the LD random seed to 2146266552 48: Generated 10 of the 10 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 0.5 48: Generated 10 of the 10 1-4 parameter combinations 48: Excluding 2 bonded neighbours molecule type 'SOL' 48: Number of degrees of freedom in T-Coupling group rest is 21.00 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 48: NVE simulation with an initial temperature of zero: will use a Verlet 48: buffer of 10%. Check your energy drift! 48: 48: 48: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/4water.gro' 48: 48: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: 48: NOTE: 10 % of the run time was spent in domain decomposition, 48: 5 % of the run time was spent in pair search, 48: you might want to increase nstlist (this has no effect on accuracy) 48: 48: Core t (s) Wall t (s) (%) 48: Time: 0.004 0.001 390.5 48: (ns/day) (hour/ns) 48: Performance: 93.871 0.256 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 48: [ OK ] MimicTest.AllQuantumMol (60 ms) 48: [ RUN ] MimicTest.TwoQuantumMol 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 48: For a correct single-point energy evaluation with nsteps = 0, use 48: continuation = yes to avoid constraining the input coordinates. 48: 48: Setting the LD random seed to 2105474039 48: Generated 10 of the 10 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 0.5 48: Generated 10 of the 10 1-4 parameter combinations 48: Excluding 2 bonded neighbours molecule type 'SOL' 48: Number of degrees of freedom in T-Coupling group rest is 21.00 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 48: NVE simulation with an initial temperature of zero: will use a Verlet 48: buffer of 10%. Check your energy drift! 48: 48: 48: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/4water.gro' 48: 48: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: 48: NOTE: 17 % of the run time was spent in domain decomposition, 48: 13 % of the run time was spent in pair search, 48: you might want to increase nstlist (this has no effect on accuracy) 48: 48: Core t (s) Wall t (s) (%) 48: Time: 0.002 0.000 380.6 48: (ns/day) (hour/ns) 48: Performance: 194.885 0.123 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 48: [ OK ] MimicTest.TwoQuantumMol (10 ms) 48: [ RUN ] MimicTest.BondCuts 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 48: For a correct single-point energy evaluation with nsteps = 0, use 48: continuation = yes to avoid constraining the input coordinates. 48: 48: Setting the LD random seed to -717443692 48: Generated 2211 of the 2211 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 0.5 48: Generated 2211 of the 2211 1-4 parameter combinations 48: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 48: Number of degrees of freedom in T-Coupling group rest is 66.00 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 48: NVE simulation: will use the initial temperature of 300.368 K for 48: determining the Verlet buffer size 48: 48: 48: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/ala.gro' 48: 48: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: 48: NOTE: 12 % of the run time was spent in domain decomposition, 48: 11 % of the run time was spent in pair search, 48: you might want to increase nstlist (this has no effect on accuracy) 48: 48: Core t (s) Wall t (s) (%) 48: Time: 0.002 0.001 387.3 48: (ns/day) (hour/ns) 48: Performance: 159.082 0.151 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 48: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm 48: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm 48: Note that mdrun will redetermine rlist based on the actual pair-list setup 48: This run will generate roughly 0 Mb of data 48: [ OK ] MimicTest.BondCuts (20 ms) 48: [----------] 4 tests from MimicTest (102 ms total) 48: 48: [----------] 1 test from MultiSimTerminationTest 48: [ RUN ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 48: [ OK ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms) 48: [----------] 1 test from MultiSimTerminationTest (0 ms total) 48: 48: [----------] 3 tests from PmeTest 48: [ RUN ] PmeTest.ReproducesEnergies 48: Setting the LD random seed to -209977513 48: Generated 8 of the 10 non-bonded parameter combinations 48: Excluding 2 bonded neighbours molecule type 'Methanol' 48: Excluding 2 bonded neighbours molecule type 'SOL' 48: Number of degrees of freedom in T-Coupling group rest is 12.00 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]: 48: NVE simulation: will use the initial temperature of 1046.791 K for 48: determining the Verlet buffer size 48: 48: Estimate for the relative computational load of the PME mesh part: 1.00 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]: 48: The optimal PME mesh load for parallel simulations is below 0.5 48: and for highly parallel simulations between 0.25 and 0.33, 48: for higher performance, increase the cut-off and the PME grid spacing. 48: 48: 48: 48: There were 2 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: Using 0 OpenMP thread per tMPI thread for PME 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting mdrun 'spc-and-methanol' 48: 20 steps, 0.0 ps. 48: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 48: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 48: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 48: Note that mdrun will redetermine rlist based on the actual pair-list setup 48: Calculating fourier grid dimensions for X Y Z 48: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 48: This run will generate roughly 0 Mb of data 48: 48: Writing final coordinates. 48: 48: Core t (s) Wall t (s) (%) 48: Time: 0.382 0.096 399.7 48: (ns/day) (hour/ns) 48: Performance: 18.979 1.265 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: Using 0 OpenMP thread per tMPI thread for PME 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting mdrun 'spc-and-methanol' 48: 20 steps, 0.0 ps. 48: 48: Writing final coordinates. 48: 48: Core t (s) Wall t (s) (%) 48: Time: 0.408 0.102 399.7 48: (ns/day) (hour/ns) 48: Performance: 17.785 1.349 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: Using 0 OpenMP thread per tMPI thread for PME 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting mdrun 'spc-and-methanol' 48: 20 steps, 0.0 ps. 48: 48: Writing final coordinates. 48: 48: Core t (s) Wall t (s) (%) 48: Time: 0.432 0.108 399.8 48: (ns/day) (hour/ns) 48: Performance: 16.782 1.430 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (883 ms) 48: [ RUN ] PmeTest.ScalesTheBox 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 48: For a correct single-point energy evaluation with nsteps = 0, use 48: continuation = yes to avoid constraining the input coordinates. 48: 48: Setting the LD random seed to 2004709839 48: Generated 8 of the 10 non-bonded parameter combinations 48: Excluding 2 bonded neighbours molecule type 'Methanol' 48: Excluding 2 bonded neighbours molecule type 'SOL' 48: Number of degrees of freedom in T-Coupling group rest is 12.00 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 48: NVE simulation: will use the initial temperature of 1046.791 K for 48: determining the Verlet buffer size 48: 48: Estimate for the relative computational load of the PME mesh part: 1.00 48: 48: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 48: The optimal PME mesh load for parallel simulations is below 0.5 48: and for highly parallel simulations between 0.25 and 0.33, 48: for higher performance, increase the cut-off and the PME grid spacing. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: Using 0 OpenMP thread per tMPI thread for PME 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting mdrun 'spc-and-methanol' 48: 0 steps, 0.0 ps. 48: 48: Core t (s) Wall t (s) (%) 48: Time: 0.004 0.001 360.4 48: (ns/day) (hour/ns) 48: Performance: 85.469 0.281 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 48: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 48: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 48: Note that mdrun will redetermine rlist based on the actual pair-list setup 48: Calculating fourier grid dimensions for X Y Z 48: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 48: This run will generate roughly 0 Mb of data 48: [ OK ] PmeTest.ScalesTheBox (91 ms) 48: [ RUN ] PmeTest.ScalesTheBoxWithWalls 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]: 48: For a correct single-point energy evaluation with nsteps = 0, use 48: continuation = yes to avoid constraining the input coordinates. 48: 48: Setting the LD random seed to 1870380694 48: Generated 8 of the 10 non-bonded parameter combinations 48: Excluding 2 bonded neighbours molecule type 'Methanol' 48: Excluding 2 bonded neighbours molecule type 'SOL' 48: Searching the wall atom type(s) 48: Number of degrees of freedom in T-Coupling group rest is 13.00 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]: 48: NVE simulation: will use the initial temperature of 966.268 K for 48: determining the Verlet buffer size 48: 48: Estimate for the relative computational load of the PME mesh part: 1.00 48: 48: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]: 48: The optimal PME mesh load for parallel simulations is below 0.5 48: and for highly parallel simulations between 0.25 and 0.33, 48: for higher performance, increase the cut-off and the PME grid spacing. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: Using 0 OpenMP thread per tMPI thread for PME 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting mdrun 'spc-and-methanol' 48: 0 steps, 0.0 ps. 48: 48: Core t (s) Wall t (s) (%) 48: Time: 0.309 0.079 391.3 48: (ns/day) (hour/ns) 48: Performance: 1.095 21.910 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 48: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 48: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 48: Note that mdrun will redetermine rlist based on the actual pair-list setup 48: Calculating fourier grid dimensions for X Y Z 48: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 48: This run will generate roughly 0 Mb of data 48: [ OK ] PmeTest.ScalesTheBoxWithWalls (1697 ms) 48: [----------] 3 tests from PmeTest (2671 ms total) 48: 48: [----------] 1 test from ReplicaExchangeTerminationTest 48: [ RUN ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 48: [ OK ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms) 48: [----------] 1 test from ReplicaExchangeTerminationTest (1 ms total) 48: 48: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 330891 of the 330891 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 0.5 48: Generated 330891 of the 330891 1-4 parameter combinations 48: Excluding 2 bonded neighbours molecule type 'SOL' 48: Number of degrees of freedom in T-Coupling group System is 27.00 48: 48: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Steepest Descents: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: 48: Energy minimization reached the maximum number of steps before the forces 48: reached the requested precision Fmax < 10. 48: 48: writing lowest energy coordinates. 48: 48: Steepest Descents did not converge to Fmax < 10 in 5 steps. 48: Potential Energy = -4.7991047e+01 48: Maximum force = 1.8629773e+02 on atom 13 48: Norm of force = 8.7721978e+01 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (510 ms) 48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 330891 of the 330891 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 0.5 48: Generated 330891 of the 330891 1-4 parameter combinations 48: Excluding 2 bonded neighbours molecule type 'SOL' 48: Number of degrees of freedom in T-Coupling group System is 27.00 48: 48: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Polak-Ribiere Conjugate Gradients: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: F-max = 3.02331e+02 on atom 3 48: F-Norm = 1.18024e+02 48: 48: 48: Energy minimization reached the maximum number of steps before the forces 48: reached the requested precision Fmax < 10. 48: 48: writing lowest energy coordinates. 48: 48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 48: Potential Energy = -5.5862068e+01 48: Maximum force = 4.2727991e+02 on atom 13 48: Norm of force = 1.8453199e+02 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (537 ms) 48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 20503 of the 20503 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 1 48: Generated 17396 of the 20503 1-4 parameter combinations 48: Excluding 3 bonded neighbours molecule type 'Glycine' 48: Number of degrees of freedom in T-Coupling group System is 22.00 48: 48: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Steepest Descents: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: 48: Energy minimization reached the maximum number of steps before the forces 48: reached the requested precision Fmax < 10. 48: 48: writing lowest energy coordinates. 48: 48: Steepest Descents did not converge to Fmax < 10 in 5 steps. 48: Potential Energy = 3.1937708e+02 48: Maximum force = 9.9988643e+03 on atom 9 48: Norm of force = 4.6166990e+03 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 turning H bonds into constraints... 48: This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (290 ms) 48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 20503 of the 20503 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 1 48: Generated 17396 of the 20503 1-4 parameter combinations 48: Excluding 3 bonded neighbours molecule type 'Glycine' 48: 48: NOTE 3 [file glycine_vacuo.top, line 12]: 48: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 48: 48: Number of degrees of freedom in T-Coupling group System is 22.00 48: 48: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 4 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Polak-Ribiere Conjugate Gradients: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: F-max = 2.41575e+04 on atom 10 48: F-Norm = 1.18451e+04 48: 48: 48: Energy minimization reached the maximum number of steps before the forces 48: reached the requested precision Fmax < 10. 48: 48: writing lowest energy coordinates. 48: 48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 48: Potential Energy = 1.5174432e+02 48: Maximum force = 7.4208867e+03 on atom 9 48: Norm of force = 3.5692995e+03 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 turning H bonds into constraints... 48: This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (203 ms) 48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 2145 of the 2145 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 0.5 48: Generated 2145 of the 2145 1-4 parameter combinations 48: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 48: 48: NOTE 3 [file unknown]: 48: You are using constraints on all bonds, whereas the forcefield has been 48: parametrized only with constraints involving hydrogen atoms. We suggest 48: using constraints = h-bonds instead, this will also improve performance. 48: 48: Cleaning up constraints and constant bonded interactions with virtual sites 48: Removed 18 Angles with virtual sites, 21 left 48: Removed 10 Proper Dih.s with virtual sites, 44 left 48: Converted 15 Constraints with virtual sites to connections, 7 left 48: Number of degrees of freedom in T-Coupling group System is 23.00 48: 48: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 4 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Steepest Descents: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: 48: Energy minimization reached the maximum number of steps before the forces 48: reached the requested precision Fmax < 10. 48: 48: writing lowest energy coordinates. 48: 48: Steepest Descents did not converge to Fmax < 10 in 5 steps. 48: Potential Energy = -1.5698462e+02 48: Maximum force = 4.5703430e+02 on atom 17 48: Norm of force = 1.8327606e+02 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 turning all bonds into constraints... 48: This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (52 ms) 48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 2145 of the 2145 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 0.5 48: Generated 2145 of the 2145 1-4 parameter combinations 48: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 48: 48: NOTE 3 [file unknown]: 48: You are using constraints on all bonds, whereas the forcefield has been 48: parametrized only with constraints involving hydrogen atoms. We suggest 48: using constraints = h-bonds instead, this will also improve performance. 48: 48: 48: NOTE 4 [file unknown]: 48: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 48: 48: Cleaning up constraints and constant bonded interactions with virtual sites 48: Removed 18 Angles with virtual sites, 21 left 48: Removed 10 Proper Dih.s with virtual sites, 44 left 48: Converted 15 Constraints with virtual sites to connections, 7 left 48: Number of degrees of freedom in T-Coupling group System is 23.00 48: 48: NOTE 5 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 5 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Polak-Ribiere Conjugate Gradients: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: F-max = 1.06799e+03 on atom 28 48: F-Norm = 4.26916e+02 48: 48: 48: Energy minimization reached the maximum number of steps before the forces 48: reached the requested precision Fmax < 10. 48: 48: writing lowest energy coordinates. 48: 48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 48: Potential Energy = -1.6941095e+02 48: Maximum force = 2.1832568e+02 on atom 17 48: Norm of force = 7.9213569e+01 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 turning all bonds into constraints... 48: This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (24 ms) 48: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (1617 ms total) 48: 48: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 1 of the 1 non-bonded parameter combinations 48: Excluding 1 bonded neighbours molecule type 'Argon' 48: Number of degrees of freedom in T-Coupling group System is 33.00 48: 48: There were 2 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Steepest Descents: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: 48: writing lowest energy coordinates. 48: 48: Steepest Descents converged to Fmax < 10 in 1 steps 48: Potential Energy = -9.7425687e-01 48: Maximum force = 4.0132279e+00 on atom 3 48: Norm of force = 1.6383933e+00 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (7 ms) 48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 1 of the 1 non-bonded parameter combinations 48: Excluding 1 bonded neighbours molecule type 'Argon' 48: Number of degrees of freedom in T-Coupling group System is 33.00 48: 48: There were 2 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Polak-Ribiere Conjugate Gradients: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: F-max = 4.01323e+00 on atom 3 48: F-Norm = 1.63839e+00 48: 48: 48: writing lowest energy coordinates. 48: 48: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 48: Potential Energy = -9.9064195e-01 48: Maximum force = 2.5781672e+00 on atom 3 48: Norm of force = 1.0525324e+00 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (12 ms) 48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: 48: WARNING 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 48: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 48: 48: Generated 1 of the 1 non-bonded parameter combinations 48: Excluding 1 bonded neighbours molecule type 'Argon' 48: Number of degrees of freedom in T-Coupling group System is 33.00 48: 48: There were 2 notes 48: 48: There was 1 warning 48: This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (4 ms) 48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 20503 of the 20503 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 1 48: Generated 17396 of the 20503 1-4 parameter combinations 48: Excluding 3 bonded neighbours molecule type 'Glycine' 48: Number of degrees of freedom in T-Coupling group System is 27.00 48: 48: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Steepest Descents: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: 48: Energy minimization reached the maximum number of steps before the forces 48: reached the requested precision Fmax < 10. 48: 48: writing lowest energy coordinates. 48: 48: Steepest Descents did not converge to Fmax < 10 in 5 steps. 48: Potential Energy = 3.1939685e+02 48: Maximum force = 9.9704248e+03 on atom 9 48: Norm of force = 4.6227568e+03 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (285 ms) 48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 20503 of the 20503 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 1 48: Generated 17396 of the 20503 1-4 parameter combinations 48: Excluding 3 bonded neighbours molecule type 'Glycine' 48: Number of degrees of freedom in T-Coupling group System is 27.00 48: 48: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Polak-Ribiere Conjugate Gradients: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: F-max = 2.41672e+04 on atom 10 48: F-Norm = 1.19357e+04 48: 48: 48: Energy minimization reached the maximum number of steps before the forces 48: reached the requested precision Fmax < 10. 48: 48: writing lowest energy coordinates. 48: 48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 48: Potential Energy = 1.5625764e+02 48: Maximum force = 7.5018237e+03 on atom 9 48: Norm of force = 3.6139019e+03 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (202 ms) 48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: 48: WARNING 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 48: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 48: 48: Generated 20503 of the 20503 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 1 48: Generated 17396 of the 20503 1-4 parameter combinations 48: Excluding 3 bonded neighbours molecule type 'Glycine' 48: Number of degrees of freedom in T-Coupling group System is 27.00 48: 48: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: 48: There was 1 warning 48: This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (231 ms) 48: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (741 ms total) 48: 48: [----------] Global test environment tear-down 48: [==========] 22 tests from 7 test cases ran. (5219 ms total) 48: [ PASSED ] 22 tests. 48: 48: YOU HAVE 4 DISABLED TESTS 48: 48/54 Test #48: MdrunMpiTests ....................... Passed 5.27 sec test 49 Start 49: MdrunMpiCoordinationTestsOneRank 49: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/mdrun-mpi-coordination-test "-ntmpi" "1" "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/MdrunMpiCoordinationTestsOneRank.xml" 49: Test timeout computed to be: 960 49: [==========] Running 27 tests from 3 test cases. 49: [----------] Global test environment set-up. 49: [----------] 1 test from BasicPropagators/PeriodicActionsTest 49: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.046 0.046 99.9 49: (ns/day) (hour/ns) 49: Performance: 31.649 0.758 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.8 49: (ns/day) (hour/ns) 49: Performance: 373.732 0.064 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.027 0.027 99.7 49: (ns/day) (hour/ns) 49: Performance: 53.716 0.447 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.1 49: (ns/day) (hour/ns) 49: Performance: 458.037 0.052 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 99.0 49: (ns/day) (hour/ns) 49: Performance: 414.464 0.058 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.006 98.7 49: (ns/day) (hour/ns) 49: Performance: 244.284 0.098 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 49: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (324 ms) 49: [----------] 1 test from BasicPropagators/PeriodicActionsTest (324 ms total) 49: 49: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.1 49: (ns/day) (hour/ns) 49: Performance: 436.612 0.055 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.3 49: (ns/day) (hour/ns) 49: Performance: 396.588 0.061 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.4 49: (ns/day) (hour/ns) 49: Performance: 433.143 0.055 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 97.9 49: (ns/day) (hour/ns) 49: Performance: 381.225 0.063 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.2 49: (ns/day) (hour/ns) 49: Performance: 389.025 0.062 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 97.7 49: (ns/day) (hour/ns) 49: Performance: 398.357 0.060 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (76 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 97.9 49: (ns/day) (hour/ns) 49: Performance: 431.928 0.056 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 98.1 49: (ns/day) (hour/ns) 49: Performance: 300.356 0.080 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 97.8 49: (ns/day) (hour/ns) 49: Performance: 425.985 0.056 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.0 49: (ns/day) (hour/ns) 49: Performance: 393.497 0.061 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.1 49: (ns/day) (hour/ns) 49: Performance: 438.196 0.055 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.005 98.7 49: (ns/day) (hour/ns) 49: Performance: 322.646 0.074 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (75 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 97.7 49: (ns/day) (hour/ns) 49: Performance: 398.641 0.060 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.5 49: (ns/day) (hour/ns) 49: Performance: 409.342 0.059 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 98.4 49: (ns/day) (hour/ns) 49: Performance: 591.171 0.041 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 98.3 49: (ns/day) (hour/ns) 49: Performance: 642.599 0.037 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.5 49: (ns/day) (hour/ns) 49: Performance: 519.969 0.046 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.6 49: (ns/day) (hour/ns) 49: Performance: 526.187 0.046 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (59 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 98.5 49: (ns/day) (hour/ns) 49: Performance: 602.798 0.040 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 98.2 49: (ns/day) (hour/ns) 49: Performance: 652.744 0.037 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.6 49: (ns/day) (hour/ns) 49: Performance: 538.655 0.045 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.021 0.021 99.7 49: (ns/day) (hour/ns) 49: Performance: 68.778 0.349 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.006 98.7 49: (ns/day) (hour/ns) 49: Performance: 242.314 0.099 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.0 49: (ns/day) (hour/ns) 49: Performance: 492.926 0.049 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (75 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.0 49: (ns/day) (hour/ns) 49: Performance: 349.617 0.069 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.006 98.3 49: (ns/day) (hour/ns) 49: Performance: 261.685 0.092 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.005 98.5 49: (ns/day) (hour/ns) 49: Performance: 322.544 0.074 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.039 0.039 99.7 49: (ns/day) (hour/ns) 49: Performance: 37.910 0.633 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 97.7 49: (ns/day) (hour/ns) 49: Performance: 305.828 0.078 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 97.9 49: (ns/day) (hour/ns) 49: Performance: 269.929 0.089 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (119 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 98.1 49: (ns/day) (hour/ns) 49: Performance: 276.173 0.087 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.013 0.013 99.2 49: (ns/day) (hour/ns) 49: Performance: 115.076 0.209 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.008 0.008 97.9 49: (ns/day) (hour/ns) 49: Performance: 182.099 0.132 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.1 49: (ns/day) (hour/ns) 49: Performance: 375.509 0.064 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.0 49: (ns/day) (hour/ns) 49: Performance: 473.128 0.051 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.1 49: (ns/day) (hour/ns) 49: Performance: 488.239 0.049 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (106 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 98.1 49: (ns/day) (hour/ns) 49: Performance: 613.727 0.039 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.1 49: (ns/day) (hour/ns) 49: Performance: 458.003 0.052 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.7 49: (ns/day) (hour/ns) 49: Performance: 333.528 0.072 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.015 0.015 99.6 49: (ns/day) (hour/ns) 49: Performance: 97.603 0.246 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.5 49: (ns/day) (hour/ns) 49: Performance: 432.353 0.056 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.6 49: (ns/day) (hour/ns) 49: Performance: 511.210 0.047 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (84 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: 49: WARNING 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Using Berendsen pressure coupling invalidates the true ensemble for the 49: thermostat 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: 49: There was 1 warning 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.3 49: (ns/day) (hour/ns) 49: Performance: 528.036 0.045 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: 49: WARNING 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Using Berendsen pressure coupling invalidates the true ensemble for the 49: thermostat 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: 49: There was 1 warning 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.3 49: (ns/day) (hour/ns) 49: Performance: 445.709 0.054 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: 49: WARNING 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Using Berendsen pressure coupling invalidates the true ensemble for the 49: thermostat 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: 49: There was 1 warning 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.4 49: (ns/day) (hour/ns) 49: Performance: 512.486 0.047 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: 49: WARNING 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Using Berendsen pressure coupling invalidates the true ensemble for the 49: thermostat 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: 49: There was 1 warning 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.2 49: (ns/day) (hour/ns) 49: Performance: 561.279 0.043 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: 49: WARNING 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Using Berendsen pressure coupling invalidates the true ensemble for the 49: thermostat 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: 49: There was 1 warning 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.4 49: (ns/day) (hour/ns) 49: Performance: 563.177 0.043 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: 49: WARNING 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Using Berendsen pressure coupling invalidates the true ensemble for the 49: thermostat 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: 49: There was 1 warning 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 99.2 49: (ns/day) (hour/ns) 49: Performance: 288.094 0.083 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (55 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.4 49: (ns/day) (hour/ns) 49: Performance: 554.958 0.043 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.4 49: (ns/day) (hour/ns) 49: Performance: 521.025 0.046 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.6 49: (ns/day) (hour/ns) 49: Performance: 447.100 0.054 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.0 49: (ns/day) (hour/ns) 49: Performance: 568.740 0.042 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.3 49: (ns/day) (hour/ns) 49: Performance: 542.640 0.044 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.3 49: (ns/day) (hour/ns) 49: Performance: 552.421 0.043 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (53 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.003 98.5 49: (ns/day) (hour/ns) 49: Performance: 580.421 0.041 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 98.4 49: (ns/day) (hour/ns) 49: Performance: 626.204 0.038 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 98.3 49: (ns/day) (hour/ns) 49: Performance: 726.485 0.033 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 98.6 49: (ns/day) (hour/ns) 49: Performance: 645.426 0.037 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.027 0.028 99.7 49: (ns/day) (hour/ns) 49: Performance: 53.309 0.450 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.004 98.2 49: (ns/day) (hour/ns) 49: Performance: 418.519 0.057 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (71 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.4 49: (ns/day) (hour/ns) 49: Performance: 456.070 0.053 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.2 49: (ns/day) (hour/ns) 49: Performance: 456.138 0.053 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 98.3 49: (ns/day) (hour/ns) 49: Performance: 618.844 0.039 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 98.4 49: (ns/day) (hour/ns) 49: Performance: 624.807 0.038 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 98.3 49: (ns/day) (hour/ns) 49: Performance: 593.392 0.040 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.4 49: (ns/day) (hour/ns) 49: Performance: 568.898 0.042 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (52 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.8 49: (ns/day) (hour/ns) 49: Performance: 494.867 0.048 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.9 49: (ns/day) (hour/ns) 49: Performance: 406.586 0.059 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.9 49: (ns/day) (hour/ns) 49: Performance: 462.333 0.052 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 98.2 49: (ns/day) (hour/ns) 49: Performance: 315.879 0.076 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 98.3 49: (ns/day) (hour/ns) 49: Performance: 278.005 0.086 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 97.8 49: (ns/day) (hour/ns) 49: Performance: 363.843 0.066 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (68 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.9 49: (ns/day) (hour/ns) 49: Performance: 329.250 0.073 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 99.4 49: (ns/day) (hour/ns) 49: Performance: 374.800 0.064 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 99.2 49: (ns/day) (hour/ns) 49: Performance: 369.340 0.065 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 99.0 49: (ns/day) (hour/ns) 49: Performance: 313.948 0.076 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 99.3 49: (ns/day) (hour/ns) 49: Performance: 330.539 0.073 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 99.1 49: (ns/day) (hour/ns) 49: Performance: 330.167 0.073 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (87 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.1 49: (ns/day) (hour/ns) 49: Performance: 331.732 0.072 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 97.9 49: (ns/day) (hour/ns) 49: Performance: 311.597 0.077 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 98.2 49: (ns/day) (hour/ns) 49: Performance: 273.076 0.088 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.006 98.4 49: (ns/day) (hour/ns) 49: Performance: 264.881 0.091 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.5 49: (ns/day) (hour/ns) 49: Performance: 426.044 0.056 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.8 49: (ns/day) (hour/ns) 49: Performance: 364.489 0.066 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (107 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 98.9 49: (ns/day) (hour/ns) 49: Performance: 588.404 0.041 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.060 0.060 99.9 49: (ns/day) (hour/ns) 49: Performance: 24.394 0.984 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.6 49: (ns/day) (hour/ns) 49: Performance: 376.864 0.064 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 99.1 49: (ns/day) (hour/ns) 49: Performance: 495.982 0.048 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 99.3 49: (ns/day) (hour/ns) 49: Performance: 522.793 0.046 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 99.2 49: (ns/day) (hour/ns) 49: Performance: 550.545 0.044 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (109 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 98.1 49: (ns/day) (hour/ns) 49: Performance: 673.583 0.036 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 98.3 49: (ns/day) (hour/ns) 49: Performance: 648.347 0.037 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.5 49: (ns/day) (hour/ns) 49: Performance: 575.111 0.042 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.6 49: (ns/day) (hour/ns) 49: Performance: 567.797 0.042 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 98.5 49: (ns/day) (hour/ns) 49: Performance: 640.128 0.037 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 97.8 49: (ns/day) (hour/ns) 49: Performance: 533.708 0.045 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (43 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 97.8 49: (ns/day) (hour/ns) 49: Performance: 402.101 0.060 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.5 49: (ns/day) (hour/ns) 49: Performance: 478.196 0.050 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.6 49: (ns/day) (hour/ns) 49: Performance: 554.409 0.043 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.6 49: (ns/day) (hour/ns) 49: Performance: 547.414 0.044 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 98.6 49: (ns/day) (hour/ns) 49: Performance: 609.537 0.039 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.7 49: (ns/day) (hour/ns) 49: Performance: 510.152 0.047 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (64 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.003 98.5 49: (ns/day) (hour/ns) 49: Performance: 585.163 0.041 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.6 49: (ns/day) (hour/ns) 49: Performance: 571.802 0.042 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.3 49: (ns/day) (hour/ns) 49: Performance: 568.583 0.042 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.5 49: (ns/day) (hour/ns) 49: Performance: 527.222 0.046 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.006 98.7 49: (ns/day) (hour/ns) 49: Performance: 267.051 0.090 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.8 49: (ns/day) (hour/ns) 49: Performance: 399.961 0.060 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (69 ms) 49: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest (1374 ms total) 49: 49: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest 49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.4 49: (ns/day) (hour/ns) 49: Performance: 524.529 0.046 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.4 49: (ns/day) (hour/ns) 49: Performance: 343.476 0.070 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.6 49: (ns/day) (hour/ns) 49: Performance: 393.146 0.061 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 98.4 49: (ns/day) (hour/ns) 49: Performance: 316.187 0.076 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 98.8 49: (ns/day) (hour/ns) 49: Performance: 269.069 0.089 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.007 0.007 98.6 49: (ns/day) (hour/ns) 49: Performance: 221.246 0.108 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (3129 ms) 49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.033 0.033 99.8 49: (ns/day) (hour/ns) 49: Performance: 44.127 0.544 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.2 49: (ns/day) (hour/ns) 49: Performance: 422.045 0.057 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.8 49: (ns/day) (hour/ns) 49: Performance: 335.325 0.072 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.007 0.007 98.3 49: (ns/day) (hour/ns) 49: Performance: 221.071 0.109 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.008 0.009 98.9 49: (ns/day) (hour/ns) 49: Performance: 171.399 0.140 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.006 99.1 49: (ns/day) (hour/ns) 49: Performance: 246.740 0.097 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (2916 ms) 49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.006 98.0 49: (ns/day) (hour/ns) 49: Performance: 258.914 0.093 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.008 0.008 98.9 49: (ns/day) (hour/ns) 49: Performance: 182.731 0.131 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 98.6 49: (ns/day) (hour/ns) 49: Performance: 272.689 0.088 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.1 49: (ns/day) (hour/ns) 49: Performance: 497.464 0.048 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.7 49: (ns/day) (hour/ns) 49: Performance: 341.458 0.070 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.054 0.054 99.8 49: (ns/day) (hour/ns) 49: Performance: 27.196 0.882 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (3047 ms) 49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.007 0.007 99.2 49: (ns/day) (hour/ns) 49: Performance: 215.300 0.111 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.005 97.6 49: (ns/day) (hour/ns) 49: Performance: 324.156 0.074 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 97.9 49: (ns/day) (hour/ns) 49: Performance: 346.627 0.069 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.6 49: (ns/day) (hour/ns) 49: Performance: 344.706 0.070 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.007 0.007 98.8 49: (ns/day) (hour/ns) 49: Performance: 199.883 0.120 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 98.7 49: (ns/day) (hour/ns) 49: Performance: 302.301 0.079 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (3153 ms) 49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.006 98.9 49: (ns/day) (hour/ns) 49: Performance: 262.734 0.091 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.008 0.008 98.9 49: (ns/day) (hour/ns) 49: Performance: 177.503 0.135 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.1 49: (ns/day) (hour/ns) 49: Performance: 335.052 0.072 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 97.9 49: (ns/day) (hour/ns) 49: Performance: 379.067 0.063 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 97.9 49: (ns/day) (hour/ns) 49: Performance: 304.980 0.079 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 97.7 49: (ns/day) (hour/ns) 49: Performance: 317.425 0.076 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (3388 ms) 49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.2 49: (ns/day) (hour/ns) 49: Performance: 379.207 0.063 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 97.6 49: (ns/day) (hour/ns) 49: Performance: 291.985 0.082 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.1 49: (ns/day) (hour/ns) 49: Performance: 449.449 0.053 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.007 0.007 98.3 49: (ns/day) (hour/ns) 49: Performance: 218.981 0.110 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 97.2 49: (ns/day) (hour/ns) 49: Performance: 379.885 0.063 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 98.7 49: (ns/day) (hour/ns) 49: Performance: 317.278 0.076 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (3392 ms) 49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 99.0 49: (ns/day) (hour/ns) 49: Performance: 329.655 0.073 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 99.1 49: (ns/day) (hour/ns) 49: Performance: 364.058 0.066 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 99.3 49: (ns/day) (hour/ns) 49: Performance: 348.548 0.069 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.007 0.007 99.5 49: (ns/day) (hour/ns) 49: Performance: 210.058 0.114 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.9 49: (ns/day) (hour/ns) 49: Performance: 379.043 0.063 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 99.2 49: (ns/day) (hour/ns) 49: Performance: 290.663 0.083 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (3002 ms) 49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 99.5 49: (ns/day) (hour/ns) 49: Performance: 275.051 0.087 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 99.4 49: (ns/day) (hour/ns) 49: Performance: 443.400 0.054 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 99.4 49: (ns/day) (hour/ns) 49: Performance: 280.282 0.086 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.006 99.2 49: (ns/day) (hour/ns) 49: Performance: 245.344 0.098 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 99.3 49: (ns/day) (hour/ns) 49: Performance: 468.878 0.051 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 99.4 49: (ns/day) (hour/ns) 49: Performance: 270.712 0.089 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (3203 ms) 49: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest (25230 ms total) 49: 49: [----------] Global test environment tear-down 49: [==========] 27 tests from 3 test cases ran. (26928 ms total) 49: [ PASSED ] 27 tests. 49/54 Test #49: MdrunMpiCoordinationTestsOneRank .... Passed 26.95 sec test 50 Start 50: MdrunMpiCoordinationTestsTwoRanks 50: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/mdrun-mpi-coordination-test "-ntmpi" "2" "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/MdrunMpiCoordinationTestsTwoRanks.xml" 50: Test timeout computed to be: 960 50: [==========] Running 27 tests from 3 test cases. 50: [----------] Global test environment set-up. 50: [----------] 1 test from BasicPropagators/PeriodicActionsTest 50: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.5%. 50: The balanceable part of the MD step is 46%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.7%. 50: 50: 50: NOTE: 46 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.021 0.011 194.1 50: (ns/day) (hour/ns) 50: Performance: 136.717 0.176 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was turned on during the run due to measured imbalance. 50: Average load imbalance: 5.3%. 50: The balanceable part of the MD step is 38%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 2.0%. 50: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 50: 50: 50: NOTE: 41 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.012 0.006 196.4 50: (ns/day) (hour/ns) 50: Performance: 240.399 0.100 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.2%. 50: The balanceable part of the MD step is 50%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.1%. 50: 50: 50: NOTE: 44 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.014 0.007 197.7 50: (ns/day) (hour/ns) 50: Performance: 200.674 0.120 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 0.6%. 50: The balanceable part of the MD step is 44%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.2%. 50: 50: 50: NOTE: 41 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.005 192.7 50: (ns/day) (hour/ns) 50: Performance: 309.344 0.078 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was turned on during the run due to measured imbalance. 50: Average load imbalance: 5.5%. 50: The balanceable part of the MD step is 38%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 2.1%. 50: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 50: 50: 50: NOTE: 41 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.004 197.2 50: (ns/day) (hour/ns) 50: Performance: 387.739 0.062 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 0.6%. 50: The balanceable part of the MD step is 53%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.3%. 50: 50: 50: NOTE: 94 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.077 0.039 199.4 50: (ns/day) (hour/ns) 50: Performance: 38.002 0.632 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 50: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (238 ms) 50: [----------] 1 test from BasicPropagators/PeriodicActionsTest (238 ms total) 50: 50: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was turned on during the run due to measured imbalance. 50: Average load imbalance: 5.8%. 50: The balanceable part of the MD step is 50%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 2.9%. 50: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 50: 50: 50: NOTE: 38 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 195.5 50: (ns/day) (hour/ns) 50: Performance: 369.384 0.065 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 0.7%. 50: The balanceable part of the MD step is 46%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.3%. 50: 50: 50: NOTE: 40 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.006 0.003 196.0 50: (ns/day) (hour/ns) 50: Performance: 467.331 0.051 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.0%. 50: The balanceable part of the MD step is 48%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.9%. 50: 50: 50: NOTE: 41 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.006 0.003 194.2 50: (ns/day) (hour/ns) 50: Performance: 442.365 0.054 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was turned on during the run due to measured imbalance. 50: Average load imbalance: 5.1%. 50: The balanceable part of the MD step is 47%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 2.4%. 50: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 50: 50: 50: NOTE: 34 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.006 0.003 196.6 50: (ns/day) (hour/ns) 50: Performance: 495.205 0.048 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.7%. 50: The balanceable part of the MD step is 1%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.0%. 50: 50: 50: NOTE: 49 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.103 0.052 199.6 50: (ns/day) (hour/ns) 50: Performance: 28.374 0.846 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 3.3%. 50: The balanceable part of the MD step is 47%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.5%. 50: 50: 50: NOTE: 40 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.005 194.5 50: (ns/day) (hour/ns) 50: Performance: 321.366 0.075 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (118 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 0.5%. 50: The balanceable part of the MD step is 48%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.2%. 50: 50: 50: NOTE: 41 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.004 195.9 50: (ns/day) (hour/ns) 50: Performance: 395.823 0.061 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was turned on during the run due to measured imbalance. 50: Average load imbalance: 12.7%. 50: The balanceable part of the MD step is 49%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 6.3%. 50: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 50: 50: NOTE: 6.3 % of the available CPU time was lost due to load imbalance 50: in the domain decomposition. 50: You can consider manually changing the decomposition (option -dd); 50: e.g. by using fewer domains along the box dimension in which there is 50: considerable inhomogeneity in the simulated system. 50: 50: NOTE: 38 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 197.2 50: (ns/day) (hour/ns) 50: Performance: 354.873 0.068 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.9%. 50: The balanceable part of the MD step is 42%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.8%. 50: 50: 50: NOTE: 39 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.006 0.003 196.1 50: (ns/day) (hour/ns) 50: Performance: 522.438 0.046 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.6%. 50: The balanceable part of the MD step is 38%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.6%. 50: 50: 50: NOTE: 49 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.095 0.048 199.5 50: (ns/day) (hour/ns) 50: Performance: 30.776 0.780 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was turned on during the run due to measured imbalance. 50: Average load imbalance: 4.6%. 50: The balanceable part of the MD step is 47%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 2.1%. 50: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 50: 50: 50: NOTE: 39 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 194.4 50: (ns/day) (hour/ns) 50: Performance: 361.484 0.066 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was turned on during the run due to measured imbalance. 50: Average load imbalance: 8.4%. 50: The balanceable part of the MD step is 50%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 4.2%. 50: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 50: 50: 50: NOTE: 39 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.004 194.9 50: (ns/day) (hour/ns) 50: Performance: 397.278 0.060 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (105 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was turned on during the run due to measured imbalance. 50: Average load imbalance: 4.3%. 50: The balanceable part of the MD step is 47%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 2.0%. 50: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 50: 50: 50: NOTE: 48 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.034 0.017 199.1 50: (ns/day) (hour/ns) 50: Performance: 85.177 0.282 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 0.8%. 50: The balanceable part of the MD step is 52%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.4%. 50: 50: 50: NOTE: 41 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.011 0.005 195.7 50: (ns/day) (hour/ns) 50: Performance: 268.219 0.089 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.2%. 50: The balanceable part of the MD step is 52%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.2%. 50: 50: 50: NOTE: 40 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.005 195.3 50: (ns/day) (hour/ns) 50: Performance: 309.905 0.077 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was turned on during the run due to measured imbalance. 50: Average load imbalance: 5.5%. 50: The balanceable part of the MD step is 52%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 2.9%. 50: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 50: 50: 50: NOTE: 44 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.014 0.007 197.3 50: (ns/day) (hour/ns) 50: Performance: 200.234 0.120 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 3.9%. 50: The balanceable part of the MD step is 49%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.9%. 50: 50: 50: NOTE: 49 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.115 0.059 194.7 50: (ns/day) (hour/ns) 50: Performance: 24.893 0.964 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 3.7%. 50: The balanceable part of the MD step is 51%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.9%. 50: 50: 50: NOTE: 40 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.014 0.007 196.1 50: (ns/day) (hour/ns) 50: Performance: 209.021 0.115 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (198 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 40 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.004 195.5 50: (ns/day) (hour/ns) 50: Performance: 336.048 0.071 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 41 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 195.9 50: (ns/day) (hour/ns) 50: Performance: 374.743 0.064 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 49 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.093 0.046 199.6 50: (ns/day) (hour/ns) 50: Performance: 31.674 0.758 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 40 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.006 0.003 194.9 50: (ns/day) (hour/ns) 50: Performance: 473.600 0.051 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 43 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.004 194.5 50: (ns/day) (hour/ns) 50: Performance: 416.242 0.058 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 39 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.004 195.3 50: (ns/day) (hour/ns) 50: Performance: 411.612 0.058 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (114 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 40 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.006 0.003 196.2 50: (ns/day) (hour/ns) 50: Performance: 459.557 0.052 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 49 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.097 0.048 199.5 50: (ns/day) (hour/ns) 50: Performance: 30.344 0.791 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 41 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.005 195.7 50: (ns/day) (hour/ns) 50: Performance: 319.409 0.075 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 40 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.003 195.4 50: (ns/day) (hour/ns) 50: Performance: 436.596 0.055 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 40 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.006 0.003 195.2 50: (ns/day) (hour/ns) 50: Performance: 454.388 0.053 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 40 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.004 193.3 50: (ns/day) (hour/ns) 50: Performance: 403.418 0.059 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (113 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 46 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.016 0.008 197.2 50: (ns/day) (hour/ns) 50: Performance: 185.326 0.130 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 40 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 195.3 50: (ns/day) (hour/ns) 50: Performance: 377.048 0.064 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 42 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 196.2 50: (ns/day) (hour/ns) 50: Performance: 359.302 0.067 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 43 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.010 0.005 195.9 50: (ns/day) (hour/ns) 50: Performance: 283.181 0.085 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 49 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.106 0.053 199.5 50: (ns/day) (hour/ns) 50: Performance: 27.644 0.868 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 39 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 193.9 50: (ns/day) (hour/ns) 50: Performance: 378.450 0.063 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (168 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 41 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.003 196.1 50: (ns/day) (hour/ns) 50: Performance: 440.830 0.054 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 40 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.006 0.003 195.0 50: (ns/day) (hour/ns) 50: Performance: 445.742 0.054 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 39 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.006 0.003 195.1 50: (ns/day) (hour/ns) 50: Performance: 483.089 0.050 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 49 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.101 0.051 199.4 50: (ns/day) (hour/ns) 50: Performance: 28.900 0.830 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 39 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.003 195.2 50: (ns/day) (hour/ns) 50: Performance: 437.527 0.055 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 38 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.003 194.8 50: (ns/day) (hour/ns) 50: Performance: 431.792 0.056 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (113 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: 50: WARNING 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Using Berendsen pressure coupling invalidates the true ensemble for the 50: thermostat 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: 50: There was 1 warning 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 39 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.003 194.7 50: (ns/day) (hour/ns) 50: Performance: 435.024 0.055 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: 50: WARNING 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Using Berendsen pressure coupling invalidates the true ensemble for the 50: thermostat 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: 50: There was 1 warning 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 39 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.006 0.003 195.8 50: (ns/day) (hour/ns) 50: Performance: 512.145 0.047 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: 50: WARNING 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Using Berendsen pressure coupling invalidates the true ensemble for the 50: thermostat 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: 50: There was 1 warning 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 97 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.090 0.045 199.4 50: (ns/day) (hour/ns) 50: Performance: 32.565 0.737 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: 50: WARNING 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Using Berendsen pressure coupling invalidates the true ensemble for the 50: thermostat 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: 50: There was 1 warning 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 39 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.004 194.9 50: (ns/day) (hour/ns) 50: Performance: 402.430 0.060 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: 50: WARNING 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Using Berendsen pressure coupling invalidates the true ensemble for the 50: thermostat 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: 50: There was 1 warning 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 38 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.006 0.003 196.2 50: (ns/day) (hour/ns) 50: Performance: 511.613 0.047 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: 50: WARNING 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Using Berendsen pressure coupling invalidates the true ensemble for the 50: thermostat 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: 50: There was 1 warning 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 41 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.005 0.003 195.9 50: (ns/day) (hour/ns) 50: Performance: 558.176 0.043 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (101 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 41 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.005 0.003 195.7 50: (ns/day) (hour/ns) 50: Performance: 556.261 0.043 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 35 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.006 0.003 193.8 50: (ns/day) (hour/ns) 50: Performance: 459.489 0.052 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 38 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.004 194.4 50: (ns/day) (hour/ns) 50: Performance: 418.277 0.057 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 40 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.004 196.1 50: (ns/day) (hour/ns) 50: Performance: 384.845 0.062 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 41 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 195.5 50: (ns/day) (hour/ns) 50: Performance: 347.860 0.069 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 39 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.006 0.003 196.2 50: (ns/day) (hour/ns) 50: Performance: 480.115 0.050 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (109 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 43 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.004 196.2 50: (ns/day) (hour/ns) 50: Performance: 405.022 0.059 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 39 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.004 195.2 50: (ns/day) (hour/ns) 50: Performance: 331.741 0.072 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 39 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.004 195.1 50: (ns/day) (hour/ns) 50: Performance: 394.543 0.061 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 39 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.004 195.1 50: (ns/day) (hour/ns) 50: Performance: 415.372 0.058 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 39 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.006 0.003 196.4 50: (ns/day) (hour/ns) 50: Performance: 458.958 0.052 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 49 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.101 0.051 199.6 50: (ns/day) (hour/ns) 50: Performance: 28.964 0.829 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (163 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 39 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 195.1 50: (ns/day) (hour/ns) 50: Performance: 369.019 0.065 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 39 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.004 194.6 50: (ns/day) (hour/ns) 50: Performance: 413.477 0.058 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 39 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.006 0.003 196.4 50: (ns/day) (hour/ns) 50: Performance: 501.636 0.048 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 39 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.006 0.003 195.7 50: (ns/day) (hour/ns) 50: Performance: 461.831 0.052 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 41 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.005 0.003 196.1 50: (ns/day) (hour/ns) 50: Performance: 583.417 0.041 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 40 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.004 193.1 50: (ns/day) (hour/ns) 50: Performance: 330.690 0.073 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (118 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 39 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.004 195.2 50: (ns/day) (hour/ns) 50: Performance: 399.377 0.060 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 38 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.003 195.0 50: (ns/day) (hour/ns) 50: Performance: 429.130 0.056 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 5 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.102 0.051 199.5 50: (ns/day) (hour/ns) 50: Performance: 28.807 0.833 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 40 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.011 0.006 194.3 50: (ns/day) (hour/ns) 50: Performance: 266.727 0.090 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 41 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.011 0.006 196.1 50: (ns/day) (hour/ns) 50: Performance: 266.312 0.090 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 42 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 196.1 50: (ns/day) (hour/ns) 50: Performance: 357.198 0.067 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (130 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was turned on during the run due to measured imbalance. 50: Average load imbalance: 6.0%. 50: The balanceable part of the MD step is 35%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 2.1%. 50: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.011 0.006 192.0 50: (ns/day) (hour/ns) 50: Performance: 257.233 0.093 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 3.1%. 50: The balanceable part of the MD step is 60%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.8%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 192.3 50: (ns/day) (hour/ns) 50: Performance: 346.402 0.069 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 0.1%. 50: The balanceable part of the MD step is 46%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.1%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.004 195.0 50: (ns/day) (hour/ns) 50: Performance: 327.091 0.073 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 0.1%. 50: The balanceable part of the MD step is 61%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.1%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.004 193.3 50: (ns/day) (hour/ns) 50: Performance: 398.550 0.060 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was turned on during the run due to measured imbalance. 50: Average load imbalance: 5.6%. 50: The balanceable part of the MD step is 54%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 3.0%. 50: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.110 0.055 199.4 50: (ns/day) (hour/ns) 50: Performance: 26.700 0.899 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 0.5%. 50: The balanceable part of the MD step is 57%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.3%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 193.7 50: (ns/day) (hour/ns) 50: Performance: 351.001 0.068 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (166 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 0.5%. 50: The balanceable part of the MD step is 55%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.3%. 50: 50: 50: NOTE: 38 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.004 193.7 50: (ns/day) (hour/ns) 50: Performance: 387.568 0.062 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 0.5%. 50: The balanceable part of the MD step is 55%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.3%. 50: 50: 50: NOTE: 40 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 196.0 50: (ns/day) (hour/ns) 50: Performance: 339.305 0.071 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 0.2%. 50: The balanceable part of the MD step is 53%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.1%. 50: 50: 50: NOTE: 94 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.105 0.053 199.3 50: (ns/day) (hour/ns) 50: Performance: 27.878 0.861 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.0%. 50: The balanceable part of the MD step is 55%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.5%. 50: 50: 50: NOTE: 39 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 194.6 50: (ns/day) (hour/ns) 50: Performance: 342.075 0.070 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 3.3%. 50: The balanceable part of the MD step is 53%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.8%. 50: 50: 50: NOTE: 39 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 194.9 50: (ns/day) (hour/ns) 50: Performance: 360.564 0.067 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was turned on during the run due to measured imbalance. 50: Average load imbalance: 4.0%. 50: The balanceable part of the MD step is 52%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 2.1%. 50: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 50: 50: 50: NOTE: 38 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.004 195.4 50: (ns/day) (hour/ns) 50: Performance: 417.427 0.057 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (122 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.003 193.5 50: (ns/day) (hour/ns) 50: Performance: 427.063 0.056 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.004 191.7 50: (ns/day) (hour/ns) 50: Performance: 402.548 0.060 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.004 192.0 50: (ns/day) (hour/ns) 50: Performance: 394.127 0.061 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.003 191.7 50: (ns/day) (hour/ns) 50: Performance: 421.468 0.057 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.003 192.0 50: (ns/day) (hour/ns) 50: Performance: 425.485 0.056 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.006 0.003 191.6 50: (ns/day) (hour/ns) 50: Performance: 443.081 0.054 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (159 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 40 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 195.4 50: (ns/day) (hour/ns) 50: Performance: 370.997 0.065 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 39 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.006 0.003 196.5 50: (ns/day) (hour/ns) 50: Performance: 473.746 0.051 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 41 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.006 0.003 194.2 50: (ns/day) (hour/ns) 50: Performance: 491.491 0.049 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 39 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.003 194.9 50: (ns/day) (hour/ns) 50: Performance: 424.971 0.056 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 40 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.003 195.0 50: (ns/day) (hour/ns) 50: Performance: 430.766 0.056 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 42 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.012 0.006 197.5 50: (ns/day) (hour/ns) 50: Performance: 249.664 0.096 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (123 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 34 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.005 196.4 50: (ns/day) (hour/ns) 50: Performance: 306.971 0.078 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 35 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 196.3 50: (ns/day) (hour/ns) 50: Performance: 368.567 0.065 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 38 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.003 193.9 50: (ns/day) (hour/ns) 50: Performance: 424.751 0.057 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 43 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.014 0.007 197.9 50: (ns/day) (hour/ns) 50: Performance: 207.396 0.116 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 39 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.006 0.003 196.2 50: (ns/day) (hour/ns) 50: Performance: 486.696 0.049 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 36 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.006 0.003 195.8 50: (ns/day) (hour/ns) 50: Performance: 454.137 0.053 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (102 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 32 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.010 0.005 196.6 50: (ns/day) (hour/ns) 50: Performance: 281.840 0.085 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.004 196.6 50: (ns/day) (hour/ns) 50: Performance: 336.838 0.071 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 37 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.004 195.5 50: (ns/day) (hour/ns) 50: Performance: 329.893 0.073 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 37 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 195.2 50: (ns/day) (hour/ns) 50: Performance: 364.672 0.066 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 35 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 196.5 50: (ns/day) (hour/ns) 50: Performance: 371.635 0.065 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 34 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.004 195.7 50: (ns/day) (hour/ns) 50: Performance: 407.905 0.059 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (121 ms) 50: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest (2343 ms total) 50: 50: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest 50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.6%. 50: The balanceable part of the MD step is 49%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.3%. 50: 50: 50: NOTE: 40 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.003 196.4 50: (ns/day) (hour/ns) 50: Performance: 440.341 0.055 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.9%. 50: The balanceable part of the MD step is 51%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.5%. 50: 50: 50: NOTE: 45 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.021 0.010 198.0 50: (ns/day) (hour/ns) 50: Performance: 140.219 0.171 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB got disabled because it was unsuitable to use. 50: Average load imbalance: 4.9%. 50: The balanceable part of the MD step is 51%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 2.5%. 50: 50: 50: NOTE: 37 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.004 195.4 50: (ns/day) (hour/ns) 50: Performance: 416.918 0.058 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB got disabled because it was unsuitable to use. 50: Average load imbalance: 11.5%. 50: The balanceable part of the MD step is 49%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 5.7%. 50: 50: NOTE: 5.7 % of the available CPU time was lost due to load imbalance 50: in the domain decomposition. 50: You might want to use dynamic load balancing (option -dlb.) 50: You can also consider manually changing the decomposition (option -dd); 50: e.g. by using fewer domains along the box dimension in which there is 50: considerable inhomogeneity in the simulated system. 50: 50: NOTE: 39 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 197.2 50: (ns/day) (hour/ns) 50: Performance: 369.906 0.065 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.9%. 50: The balanceable part of the MD step is 51%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.5%. 50: 50: 50: NOTE: 39 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.005 196.4 50: (ns/day) (hour/ns) 50: Performance: 313.341 0.077 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 3.8%. 50: The balanceable part of the MD step is 50%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.9%. 50: 50: 50: NOTE: 40 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.004 196.0 50: (ns/day) (hour/ns) 50: Performance: 390.244 0.061 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (3594 ms) 50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.9%. 50: The balanceable part of the MD step is 50%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.9%. 50: 50: 50: NOTE: 42 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 194.8 50: (ns/day) (hour/ns) 50: Performance: 349.052 0.069 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.5%. 50: The balanceable part of the MD step is 50%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.2%. 50: 50: 50: NOTE: 91 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.057 0.029 199.0 50: (ns/day) (hour/ns) 50: Performance: 51.152 0.469 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.8%. 50: The balanceable part of the MD step is 54%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.0%. 50: 50: 50: NOTE: 42 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.012 0.006 196.2 50: (ns/day) (hour/ns) 50: Performance: 244.628 0.098 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.1%. 50: The balanceable part of the MD step is 50%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.1%. 50: 50: 50: NOTE: 43 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.015 0.008 196.7 50: (ns/day) (hour/ns) 50: Performance: 195.215 0.123 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.8%. 50: The balanceable part of the MD step is 54%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.0%. 50: 50: 50: NOTE: 41 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.010 0.005 195.9 50: (ns/day) (hour/ns) 50: Performance: 283.990 0.085 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 0.7%. 50: The balanceable part of the MD step is 54%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.4%. 50: 50: 50: NOTE: 37 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 195.8 50: (ns/day) (hour/ns) 50: Performance: 360.617 0.067 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (3177 ms) 50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.010 0.005 196.8 50: (ns/day) (hour/ns) 50: Performance: 301.790 0.080 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.004 196.2 50: (ns/day) (hour/ns) 50: Performance: 387.532 0.062 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.010 0.005 195.4 50: (ns/day) (hour/ns) 50: Performance: 300.627 0.080 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.005 195.9 50: (ns/day) (hour/ns) 50: Performance: 312.927 0.077 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.026 0.013 198.5 50: (ns/day) (hour/ns) 50: Performance: 113.493 0.211 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 196.6 50: (ns/day) (hour/ns) 50: Performance: 350.223 0.069 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (3034 ms) 50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.004 194.1 50: (ns/day) (hour/ns) 50: Performance: 416.862 0.058 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.005 195.1 50: (ns/day) (hour/ns) 50: Performance: 317.933 0.075 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.010 0.005 195.8 50: (ns/day) (hour/ns) 50: Performance: 300.906 0.080 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.478 0.239 199.9 50: (ns/day) (hour/ns) 50: Performance: 6.139 3.909 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.015 0.008 197.4 50: (ns/day) (hour/ns) 50: Performance: 194.617 0.123 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.097 0.049 199.3 50: (ns/day) (hour/ns) 50: Performance: 30.122 0.797 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (3367 ms) 50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.012 0.006 196.0 50: (ns/day) (hour/ns) 50: Performance: 245.047 0.098 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.058 0.029 199.2 50: (ns/day) (hour/ns) 50: Performance: 50.827 0.472 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.017 0.009 197.8 50: (ns/day) (hour/ns) 50: Performance: 166.879 0.144 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.015 0.008 198.3 50: (ns/day) (hour/ns) 50: Performance: 195.488 0.123 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.005 196.5 50: (ns/day) (hour/ns) 50: Performance: 325.467 0.074 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.686 0.343 199.9 50: (ns/day) (hour/ns) 50: Performance: 4.282 5.605 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (3286 ms) 50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.020 0.010 197.3 50: (ns/day) (hour/ns) 50: Performance: 148.582 0.162 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.005 193.9 50: (ns/day) (hour/ns) 50: Performance: 321.610 0.075 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.076 0.038 199.4 50: (ns/day) (hour/ns) 50: Performance: 38.685 0.620 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.011 0.005 196.2 50: (ns/day) (hour/ns) 50: Performance: 269.063 0.089 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.016 0.008 196.3 50: (ns/day) (hour/ns) 50: Performance: 185.991 0.129 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.011 0.006 196.2 50: (ns/day) (hour/ns) 50: Performance: 263.758 0.091 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (3607 ms) 50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.5%. 50: The balanceable part of the MD step is 3%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.0%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.066 0.033 198.5 50: (ns/day) (hour/ns) 50: Performance: 44.418 0.540 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.2%. 50: The balanceable part of the MD step is 59%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.3%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 192.3 50: (ns/day) (hour/ns) 50: Performance: 343.180 0.070 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.5%. 50: The balanceable part of the MD step is 53%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.8%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.011 0.006 192.8 50: (ns/day) (hour/ns) 50: Performance: 251.885 0.095 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 0.7%. 50: The balanceable part of the MD step is 62%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.4%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.005 193.0 50: (ns/day) (hour/ns) 50: Performance: 312.277 0.077 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 0.6%. 50: The balanceable part of the MD step is 61%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.4%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.014 0.007 193.8 50: (ns/day) (hour/ns) 50: Performance: 197.407 0.122 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.8%. 50: The balanceable part of the MD step is 53%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.5%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.015 0.008 193.8 50: (ns/day) (hour/ns) 50: Performance: 193.550 0.124 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (3936 ms) 50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.010 0.005 195.3 50: (ns/day) (hour/ns) 50: Performance: 291.364 0.082 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.011 0.006 195.2 50: (ns/day) (hour/ns) 50: Performance: 258.349 0.093 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.010 0.005 193.4 50: (ns/day) (hour/ns) 50: Performance: 272.231 0.088 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.012 0.006 194.0 50: (ns/day) (hour/ns) 50: Performance: 243.531 0.099 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.125 0.063 198.1 50: (ns/day) (hour/ns) 50: Performance: 23.317 1.029 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.010 0.005 193.3 50: (ns/day) (hour/ns) 50: Performance: 295.593 0.081 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (3566 ms) 50: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest (27567 ms total) 50: 50: [----------] Global test environment tear-down 50: [==========] 27 tests from 3 test cases ran. (30148 ms total) 50: [ PASSED ] 27 tests. 50/54 Test #50: MdrunMpiCoordinationTestsTwoRanks ... Passed 30.16 sec test 51 Start 51: GmxapiExternalInterfaceTests 51: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/GmxapiExternalInterfaceTests.xml" 51: Test timeout computed to be: 600 51: [==========] Running 9 tests from 2 test cases. 51: [----------] Global test environment set-up. 51: [----------] 8 tests from GmxApiTest 51: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD 51: Setting the LD random seed to -138416244 51: Generated 331705 of the 331705 non-bonded parameter combinations 51: Generating 1-4 interactions: fudge = 0.5 51: Generated 331705 of the 331705 1-4 parameter combinations 51: Excluding 2 bonded neighbours molecule type 'SOL' 51: Excluding 3 bonded neighbours molecule type 'methane' 51: 51: NOTE 1 [file spc_and_methane.top, line 33]: 51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 51: the time step of 2.0e-03 ps. 51: Maybe you forgot to change the constraints mdp option. 51: 51: Number of degrees of freedom in T-Coupling group System is 18.00 51: 51: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 51: You are using a plain Coulomb cut-off, which might produce artifacts. 51: You might want to consider using PME electrostatics. 51: 51: 51: 51: There were 2 notes 51: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 51: log). 51: The current CPU can measure timings more accurately than the code in 51: gmxapi-test was configured to use. This might affect your simulation 51: speed as accurate timings are needed for load-balancing. 51: Please consider rebuilding gmxapi-test with the GMX_USE_RDTSCP=ON CMake option. 51: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296 51: 51: 51: Using 1 MPI thread 51: 51: Non-default thread affinity set, disabling internal thread affinity 51: 51: Using 2 OpenMP threads 51: 51: starting mdrun 'Water and methane' 51: 2 steps, 0.0 ps. 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: This run will generate roughly 0 Mb of data 51: 51: Writing final coordinates. 51: 51: Core t (s) Wall t (s) (%) 51: Time: 0.008 0.004 180.5 51: (ns/day) (hour/ns) 51: Performance: 120.066 0.200 51: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (680 ms) 51: [ RUN ] GmxApiTest.SystemConstruction 51: Setting the LD random seed to -738497793 51: Generated 331705 of the 331705 non-bonded parameter combinations 51: Generating 1-4 interactions: fudge = 0.5 51: Generated 331705 of the 331705 1-4 parameter combinations 51: Excluding 2 bonded neighbours molecule type 'SOL' 51: Excluding 3 bonded neighbours molecule type 'methane' 51: 51: NOTE 1 [file spc_and_methane.top, line 33]: 51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 51: the time step of 2.0e-03 ps. 51: Maybe you forgot to change the constraints mdp option. 51: 51: Number of degrees of freedom in T-Coupling group System is 18.00 51: 51: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 51: You are using a plain Coulomb cut-off, which might produce artifacts. 51: You might want to consider using PME electrostatics. 51: 51: 51: 51: There were 2 notes 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: This run will generate roughly 0 Mb of data 51: [ OK ] GmxApiTest.SystemConstruction (516 ms) 51: [ RUN ] GmxApiTest.SaneVersionComparisons 51: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) 51: [ RUN ] GmxApiTest.VersionNamed0_1_Features 51: [ OK ] GmxApiTest.VersionNamed0_1_Features (1 ms) 51: [ RUN ] GmxApiTest.RunnerBasicMD 51: Setting the LD random seed to -168951873 51: Generated 331705 of the 331705 non-bonded parameter combinations 51: Generating 1-4 interactions: fudge = 0.5 51: Generated 331705 of the 331705 1-4 parameter combinations 51: Excluding 2 bonded neighbours molecule type 'SOL' 51: Excluding 3 bonded neighbours molecule type 'methane' 51: 51: NOTE 1 [file spc_and_methane.top, line 33]: 51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 51: the time step of 2.0e-03 ps. 51: Maybe you forgot to change the constraints mdp option. 51: 51: Number of degrees of freedom in T-Coupling group System is 18.00 51: 51: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 51: You are using a plain Coulomb cut-off, which might produce artifacts. 51: You might want to consider using PME electrostatics. 51: 51: 51: 51: There were 2 notes 51: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 51: log). 51: The current CPU can measure timings more accurately than the code in 51: gmxapi-test was configured to use. This might affect your simulation 51: speed as accurate timings are needed for load-balancing. 51: Please consider rebuilding gmxapi-test with the GMX_USE_RDTSCP=ON CMake option. 51: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296 51: 51: 51: Using 1 MPI thread 51: 51: Non-default thread affinity set, disabling internal thread affinity 51: 51: Using 2 OpenMP threads 51: 51: starting mdrun 'Water and methane' 51: 2 steps, 0.0 ps. 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: This run will generate roughly 0 Mb of data 51: 51: Writing final coordinates. 51: 51: Core t (s) Wall t (s) (%) 51: Time: 0.012 0.006 196.2 51: (ns/day) (hour/ns) 51: Performance: 83.967 0.286 51: [ OK ] GmxApiTest.RunnerBasicMD (515 ms) 51: [ RUN ] GmxApiTest.RunnerReinitialize 51: Setting the LD random seed to -270663761 51: Generated 331705 of the 331705 non-bonded parameter combinations 51: Generating 1-4 interactions: fudge = 0.5 51: Generated 331705 of the 331705 1-4 parameter combinations 51: Excluding 2 bonded neighbours molecule type 'SOL' 51: Excluding 3 bonded neighbours molecule type 'methane' 51: 51: NOTE 1 [file spc_and_methane.top, line 33]: 51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 51: the time step of 2.0e-03 ps. 51: Maybe you forgot to change the constraints mdp option. 51: 51: Number of degrees of freedom in T-Coupling group System is 18.00 51: 51: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 51: You are using a plain Coulomb cut-off, which might produce artifacts. 51: You might want to consider using PME electrostatics. 51: 51: 51: 51: There were 2 notes 51: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 51: log). 51: The current CPU can measure timings more accurately than the code in 51: gmxapi-test was configured to use. This might affect your simulation 51: speed as accurate timings are needed for load-balancing. 51: Please consider rebuilding gmxapi-test with the GMX_USE_RDTSCP=ON CMake option. 51: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296 51: 51: 51: Using 1 MPI thread 51: 51: Non-default thread affinity set, disabling internal thread affinity 51: 51: Using 2 OpenMP threads 51: 51: starting mdrun 'Water and methane' 51: 20 steps, 0.0 ps. 51: 51: 51: Received the remote INT/TERM signal, stopping within 50 steps 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: This run will generate roughly 0 Mb of data 51: 51: Writing final coordinates. 51: 51: Core t (s) Wall t (s) (%) 51: Time: 0.057 0.028 199.3 51: (ns/day) (hour/ns) 51: Performance: 124.469 0.193 51: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 51: log). 51: The current CPU can measure timings more accurately than the code in 51: gmxapi-test was configured to use. This might affect your simulation 51: speed as accurate timings are needed for load-balancing. 51: Please consider rebuilding gmxapi-test with the GMX_USE_RDTSCP=ON CMake option. 51: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296 51: 51: 51: Using 1 MPI thread 51: 51: Non-default thread affinity set, disabling internal thread affinity 51: 51: Using 2 OpenMP threads 51: 51: starting mdrun 'Water and methane' 51: 20 steps, 0.0 ps. 51: 51: Writing final coordinates. 51: 51: Core t (s) Wall t (s) (%) 51: Time: 0.009 0.005 197.0 51: (ns/day) (hour/ns) 51: Performance: 778.809 0.031 51: [ OK ] GmxApiTest.RunnerReinitialize (567 ms) 51: [ RUN ] GmxApiTest.RunnerContinuedMD 51: Setting the LD random seed to -26542154 51: Generated 331705 of the 331705 non-bonded parameter combinations 51: Generating 1-4 interactions: fudge = 0.5 51: Generated 331705 of the 331705 1-4 parameter combinations 51: Excluding 2 bonded neighbours molecule type 'SOL' 51: Excluding 3 bonded neighbours molecule type 'methane' 51: 51: NOTE 1 [file spc_and_methane.top, line 33]: 51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 51: the time step of 2.0e-03 ps. 51: Maybe you forgot to change the constraints mdp option. 51: 51: Number of degrees of freedom in T-Coupling group System is 18.00 51: 51: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD_input.mdp]: 51: You are using a plain Coulomb cut-off, which might produce artifacts. 51: You might want to consider using PME electrostatics. 51: 51: 51: 51: There were 2 notes 51: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 51: log). 51: The current CPU can measure timings more accurately than the code in 51: gmxapi-test was configured to use. This might affect your simulation 51: speed as accurate timings are needed for load-balancing. 51: Please consider rebuilding gmxapi-test with the GMX_USE_RDTSCP=ON CMake option. 51: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296 51: 51: 51: Using 1 MPI thread 51: 51: Non-default thread affinity set, disabling internal thread affinity 51: 51: Using 2 OpenMP threads 51: 51: starting mdrun 'Water and methane' 51: 10 steps, 0.0 ps. 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: This run will generate roughly 0 Mb of data 51: 51: Writing final coordinates. 51: 51: Core t (s) Wall t (s) (%) 51: Time: 0.056 0.028 199.1 51: (ns/day) (hour/ns) 51: Performance: 66.492 0.361 51: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 51: log). 51: The current CPU can measure timings more accurately than the code in 51: gmxapi-test was configured to use. This might affect your simulation 51: speed as accurate timings are needed for load-balancing. 51: Please consider rebuilding gmxapi-test with the GMX_USE_RDTSCP=ON CMake option. 51: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 51: 51: Overriding nsteps with value passed on the command line: 20 steps, 0.0391 ps 51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296 51: 51: 51: Using 1 MPI thread 51: 51: Non-default thread affinity set, disabling internal thread affinity 51: 51: Using 2 OpenMP threads 51: 51: starting mdrun 'Water and methane' 51: 20 steps, 0.0 ps. 51: 51: Writing final coordinates. 51: 51: Core t (s) Wall t (s) (%) 51: Time: 0.011 0.005 196.1 51: (ns/day) (hour/ns) 51: Performance: 660.985 0.036 51: [ OK ] GmxApiTest.RunnerContinuedMD (602 ms) 51: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient 51: Setting the LD random seed to -625379329 51: Generated 331705 of the 331705 non-bonded parameter combinations 51: Generating 1-4 interactions: fudge = 0.5 51: Generated 331705 of the 331705 1-4 parameter combinations 51: Excluding 2 bonded neighbours molecule type 'SOL' 51: Excluding 3 bonded neighbours molecule type 'methane' 51: 51: NOTE 1 [file spc_and_methane.top, line 33]: 51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 51: the time step of 2.0e-03 ps. 51: Maybe you forgot to change the constraints mdp option. 51: 51: Number of degrees of freedom in T-Coupling group System is 18.00 51: 51: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 51: You are using a plain Coulomb cut-off, which might produce artifacts. 51: You might want to consider using PME electrostatics. 51: 51: 51: 51: There were 2 notes 51: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 51: log). 51: The current CPU can measure timings more accurately than the code in 51: gmxapi-test was configured to use. This might affect your simulation 51: speed as accurate timings are needed for load-balancing. 51: Please consider rebuilding gmxapi-test with the GMX_USE_RDTSCP=ON CMake option. 51: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 51: Changing nstlist from 10 to 1, rlist from 1.041 to 1 51: 51: 51: Using 1 MPI thread 51: 51: Non-default thread affinity set, disabling internal thread affinity 51: 51: Using 2 OpenMP threads 51: 51: starting mdrun 'Water and methane' 51: 1 steps, 0.0 ps. 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: This run will generate roughly 0 Mb of data 51: 51: Writing final coordinates. 51: 51: Core t (s) Wall t (s) (%) 51: Time: 0.069 0.035 198.7 51: (ns/day) (hour/ns) 51: Performance: 9.758 2.460 51: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 51: log). 51: The current CPU can measure timings more accurately than the code in 51: gmxapi-test was configured to use. This might affect your simulation 51: speed as accurate timings are needed for load-balancing. 51: Please consider rebuilding gmxapi-test with the GMX_USE_RDTSCP=ON CMake option. 51: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 51: 51: Overriding nsteps with value passed on the command line: 2 steps, 0.00391 ps 51: Changing nstlist from 10 to 1, rlist from 1.041 to 1 51: 51: 51: Using 1 MPI thread 51: 51: Non-default thread affinity set, disabling internal thread affinity 51: 51: Using 2 OpenMP threads 51: 51: starting mdrun 'Water and methane' 51: 2 steps, 0.0 ps. 51: 51: Core t (s) Wall t (s) (%) 51: Time: 0.010 0.005 183.3 51: (ns/day) (hour/ns) 51: Performance: 64.547 0.372 51: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (604 ms) 51: [----------] 8 tests from GmxApiTest (3485 ms total) 51: 51: [----------] 1 test from GmxApiBasicTest 51: [ RUN ] GmxApiBasicTest.Status 51: [ OK ] GmxApiBasicTest.Status (0 ms) 51: [----------] 1 test from GmxApiBasicTest (0 ms total) 51: 51: [----------] Global test environment tear-down 51: [==========] 9 tests from 2 test cases ran. (3485 ms total) 51: [ PASSED ] 9 tests. 51/54 Test #51: GmxapiExternalInterfaceTests ........ Passed 3.51 sec test 52 Start 52: GmxapiMpiTests 52: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/gmxapi-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/GmxapiMpiTests.xml" 52: Test timeout computed to be: 600 52: [==========] Running 9 tests from 2 test cases. 52: [----------] Global test environment set-up. 52: [----------] 8 tests from GmxApiTest 52: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD 52: Setting the LD random seed to -201326662 52: Generated 331705 of the 331705 non-bonded parameter combinations 52: Generating 1-4 interactions: fudge = 0.5 52: Generated 331705 of the 331705 1-4 parameter combinations 52: Excluding 2 bonded neighbours molecule type 'SOL' 52: Excluding 3 bonded neighbours molecule type 'methane' 52: 52: NOTE 1 [file spc_and_methane.top, line 33]: 52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 52: the time step of 2.0e-03 ps. 52: Maybe you forgot to change the constraints mdp option. 52: 52: Number of degrees of freedom in T-Coupling group System is 18.00 52: 52: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 52: You are using a plain Coulomb cut-off, which might produce artifacts. 52: You might want to consider using PME electrostatics. 52: 52: 52: 52: There were 2 notes 52: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 52: log). 52: The current CPU can measure timings more accurately than the code in 52: gmxapi-mpi-test was configured to use. This might affect your simulation 52: speed as accurate timings are needed for load-balancing. 52: Please consider rebuilding gmxapi-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 52: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296 52: 52: 52: Using 1 MPI thread 52: 52: Non-default thread affinity set, disabling internal thread affinity 52: 52: Using 2 OpenMP threads 52: 52: starting mdrun 'Water and methane' 52: 2 steps, 0.0 ps. 52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 52: Note that mdrun will redetermine rlist based on the actual pair-list setup 52: This run will generate roughly 0 Mb of data 52: 52: Writing final coordinates. 52: 52: Core t (s) Wall t (s) (%) 52: Time: 0.012 0.006 196.7 52: (ns/day) (hour/ns) 52: Performance: 84.667 0.283 52: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (669 ms) 52: [ RUN ] GmxApiTest.SystemConstruction 52: Setting the LD random seed to -805306371 52: Generated 331705 of the 331705 non-bonded parameter combinations 52: Generating 1-4 interactions: fudge = 0.5 52: Generated 331705 of the 331705 1-4 parameter combinations 52: Excluding 2 bonded neighbours molecule type 'SOL' 52: Excluding 3 bonded neighbours molecule type 'methane' 52: 52: NOTE 1 [file spc_and_methane.top, line 33]: 52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 52: the time step of 2.0e-03 ps. 52: Maybe you forgot to change the constraints mdp option. 52: 52: Number of degrees of freedom in T-Coupling group System is 18.00 52: 52: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 52: You are using a plain Coulomb cut-off, which might produce artifacts. 52: You might want to consider using PME electrostatics. 52: 52: 52: 52: There were 2 notes 52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 52: Note that mdrun will redetermine rlist based on the actual pair-list setup 52: This run will generate roughly 0 Mb of data 52: [ OK ] GmxApiTest.SystemConstruction (516 ms) 52: [ RUN ] GmxApiTest.SaneVersionComparisons 52: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) 52: [ RUN ] GmxApiTest.VersionNamed0_1_Features 52: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) 52: [ RUN ] GmxApiTest.RunnerBasicMD 52: Setting the LD random seed to -5472545 52: Generated 331705 of the 331705 non-bonded parameter combinations 52: Generating 1-4 interactions: fudge = 0.5 52: Generated 331705 of the 331705 1-4 parameter combinations 52: Excluding 2 bonded neighbours molecule type 'SOL' 52: Excluding 3 bonded neighbours molecule type 'methane' 52: 52: NOTE 1 [file spc_and_methane.top, line 33]: 52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 52: the time step of 2.0e-03 ps. 52: Maybe you forgot to change the constraints mdp option. 52: 52: Number of degrees of freedom in T-Coupling group System is 18.00 52: 52: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 52: You are using a plain Coulomb cut-off, which might produce artifacts. 52: You might want to consider using PME electrostatics. 52: 52: 52: 52: There were 2 notes 52: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 52: log). 52: The current CPU can measure timings more accurately than the code in 52: gmxapi-mpi-test was configured to use. This might affect your simulation 52: speed as accurate timings are needed for load-balancing. 52: Please consider rebuilding gmxapi-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 52: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296 52: 52: 52: Using 1 MPI thread 52: 52: Non-default thread affinity set, disabling internal thread affinity 52: 52: Using 2 OpenMP threads 52: 52: starting mdrun 'Water and methane' 52: 2 steps, 0.0 ps. 52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 52: Note that mdrun will redetermine rlist based on the actual pair-list setup 52: This run will generate roughly 0 Mb of data 52: 52: Writing final coordinates. 52: 52: Core t (s) Wall t (s) (%) 52: Time: 0.008 0.004 181.3 52: (ns/day) (hour/ns) 52: Performance: 121.377 0.198 52: [ OK ] GmxApiTest.RunnerBasicMD (487 ms) 52: [ RUN ] GmxApiTest.RunnerReinitialize 52: Setting the LD random seed to -1074382050 52: Generated 331705 of the 331705 non-bonded parameter combinations 52: Generating 1-4 interactions: fudge = 0.5 52: Generated 331705 of the 331705 1-4 parameter combinations 52: Excluding 2 bonded neighbours molecule type 'SOL' 52: Excluding 3 bonded neighbours molecule type 'methane' 52: 52: NOTE 1 [file spc_and_methane.top, line 33]: 52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 52: the time step of 2.0e-03 ps. 52: Maybe you forgot to change the constraints mdp option. 52: 52: Number of degrees of freedom in T-Coupling group System is 18.00 52: 52: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 52: You are using a plain Coulomb cut-off, which might produce artifacts. 52: You might want to consider using PME electrostatics. 52: 52: 52: 52: There were 2 notes 52: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 52: log). 52: The current CPU can measure timings more accurately than the code in 52: gmxapi-mpi-test was configured to use. This might affect your simulation 52: speed as accurate timings are needed for load-balancing. 52: Please consider rebuilding gmxapi-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 52: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296 52: 52: 52: Using 1 MPI thread 52: 52: Non-default thread affinity set, disabling internal thread affinity 52: 52: Using 2 OpenMP threads 52: 52: starting mdrun 'Water and methane' 52: 20 steps, 0.0 ps. 52: 52: 52: Received the remote INT/TERM signal, stopping within 50 steps 52: 52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 52: Note that mdrun will redetermine rlist based on the actual pair-list setup 52: This run will generate roughly 0 Mb of data 52: 52: Writing final coordinates. 52: 52: Core t (s) Wall t (s) (%) 52: Time: 0.014 0.007 196.5 52: (ns/day) (hour/ns) 52: Performance: 485.864 0.049 52: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 52: log). 52: The current CPU can measure timings more accurately than the code in 52: gmxapi-mpi-test was configured to use. This might affect your simulation 52: speed as accurate timings are needed for load-balancing. 52: Please consider rebuilding gmxapi-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 52: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296 52: 52: 52: Using 1 MPI thread 52: 52: Non-default thread affinity set, disabling internal thread affinity 52: 52: Using 2 OpenMP threads 52: 52: starting mdrun 'Water and methane' 52: 20 steps, 0.0 ps. 52: 52: Writing final coordinates. 52: 52: Core t (s) Wall t (s) (%) 52: Time: 0.012 0.006 196.7 52: (ns/day) (hour/ns) 52: Performance: 579.499 0.041 52: [ OK ] GmxApiTest.RunnerReinitialize (604 ms) 52: [ RUN ] GmxApiTest.RunnerContinuedMD 52: Setting the LD random seed to 889019326 52: Generated 331705 of the 331705 non-bonded parameter combinations 52: Generating 1-4 interactions: fudge = 0.5 52: Generated 331705 of the 331705 1-4 parameter combinations 52: Excluding 2 bonded neighbours molecule type 'SOL' 52: Excluding 3 bonded neighbours molecule type 'methane' 52: 52: NOTE 1 [file spc_and_methane.top, line 33]: 52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 52: the time step of 2.0e-03 ps. 52: Maybe you forgot to change the constraints mdp option. 52: 52: Number of degrees of freedom in T-Coupling group System is 18.00 52: 52: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD_input.mdp]: 52: You are using a plain Coulomb cut-off, which might produce artifacts. 52: You might want to consider using PME electrostatics. 52: 52: 52: 52: There were 2 notes 52: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 52: log). 52: The current CPU can measure timings more accurately than the code in 52: gmxapi-mpi-test was configured to use. This might affect your simulation 52: speed as accurate timings are needed for load-balancing. 52: Please consider rebuilding gmxapi-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 52: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296 52: 52: 52: Using 1 MPI thread 52: 52: Non-default thread affinity set, disabling internal thread affinity 52: 52: Using 2 OpenMP threads 52: 52: starting mdrun 'Water and methane' 52: 10 steps, 0.0 ps. 52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 52: Note that mdrun will redetermine rlist based on the actual pair-list setup 52: This run will generate roughly 0 Mb of data 52: 52: Writing final coordinates. 52: 52: Core t (s) Wall t (s) (%) 52: Time: 0.021 0.011 198.2 52: (ns/day) (hour/ns) 52: Performance: 175.112 0.137 52: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 52: log). 52: The current CPU can measure timings more accurately than the code in 52: gmxapi-mpi-test was configured to use. This might affect your simulation 52: speed as accurate timings are needed for load-balancing. 52: Please consider rebuilding gmxapi-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 52: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 52: 52: Overriding nsteps with value passed on the command line: 20 steps, 0.0391 ps 52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296 52: 52: 52: Using 1 MPI thread 52: 52: Non-default thread affinity set, disabling internal thread affinity 52: 52: Using 2 OpenMP threads 52: 52: starting mdrun 'Water and methane' 52: 20 steps, 0.0 ps. 52: 52: Writing final coordinates. 52: 52: Core t (s) Wall t (s) (%) 52: Time: 0.010 0.005 196.6 52: (ns/day) (hour/ns) 52: Performance: 664.501 0.036 52: [ OK ] GmxApiTest.RunnerContinuedMD (705 ms) 52: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient 52: Setting the LD random seed to 2123758759 52: Generated 331705 of the 331705 non-bonded parameter combinations 52: Generating 1-4 interactions: fudge = 0.5 52: Generated 331705 of the 331705 1-4 parameter combinations 52: Excluding 2 bonded neighbours molecule type 'SOL' 52: Excluding 3 bonded neighbours molecule type 'methane' 52: 52: NOTE 1 [file spc_and_methane.top, line 33]: 52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 52: the time step of 2.0e-03 ps. 52: Maybe you forgot to change the constraints mdp option. 52: 52: Number of degrees of freedom in T-Coupling group System is 18.00 52: 52: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 52: You are using a plain Coulomb cut-off, which might produce artifacts. 52: You might want to consider using PME electrostatics. 52: 52: 52: 52: There were 2 notes 52: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 52: log). 52: The current CPU can measure timings more accurately than the code in 52: gmxapi-mpi-test was configured to use. This might affect your simulation 52: speed as accurate timings are needed for load-balancing. 52: Please consider rebuilding gmxapi-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 52: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 52: Changing nstlist from 10 to 1, rlist from 1.041 to 1 52: 52: 52: Using 1 MPI thread 52: 52: Non-default thread affinity set, disabling internal thread affinity 52: 52: Using 2 OpenMP threads 52: 52: starting mdrun 'Water and methane' 52: 1 steps, 0.0 ps. 52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 52: Note that mdrun will redetermine rlist based on the actual pair-list setup 52: This run will generate roughly 0 Mb of data 52: 52: Writing final coordinates. 52: 52: Core t (s) Wall t (s) (%) 52: Time: 0.007 0.004 195.1 52: (ns/day) (hour/ns) 52: Performance: 90.308 0.266 52: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 52: log). 52: The current CPU can measure timings more accurately than the code in 52: gmxapi-mpi-test was configured to use. This might affect your simulation 52: speed as accurate timings are needed for load-balancing. 52: Please consider rebuilding gmxapi-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 52: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.6-Debian-2020.6-2 (single precision) 52: 52: Overriding nsteps with value passed on the command line: 2 steps, 0.00391 ps 52: Changing nstlist from 10 to 1, rlist from 1.041 to 1 52: 52: 52: Using 1 MPI thread 52: 52: Non-default thread affinity set, disabling internal thread affinity 52: 52: Using 2 OpenMP threads 52: 52: starting mdrun 'Water and methane' 52: 2 steps, 0.0 ps. 52: 52: Core t (s) Wall t (s) (%) 52: Time: 0.061 0.030 199.4 52: (ns/day) (hour/ns) 52: Performance: 11.084 2.165 52: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (673 ms) 52: [----------] 8 tests from GmxApiTest (3657 ms total) 52: 52: [----------] 1 test from GmxApiBasicTest 52: [ RUN ] GmxApiBasicTest.Status 52: [ OK ] GmxApiBasicTest.Status (0 ms) 52: [----------] 1 test from GmxApiBasicTest (0 ms total) 52: 52: [----------] Global test environment tear-down 52: [==========] 9 tests from 2 test cases ran. (3657 ms total) 52: [ PASSED ] 9 tests. 52/54 Test #52: GmxapiMpiTests ...................... Passed 3.68 sec test 53 Start 53: GmxapiInternalInterfaceTests 53: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/GmxapiInternalInterfaceTests.xml" 53: Test timeout computed to be: 600 53: [==========] Running 2 tests from 1 test case. 53: [----------] Global test environment set-up. 53: [----------] 2 tests from GmxApiTest 53: [ RUN ] GmxApiTest.BuildApiWorkflowImpl 53: Setting the LD random seed to -4721192 53: Generated 331705 of the 331705 non-bonded parameter combinations 53: Generating 1-4 interactions: fudge = 0.5 53: Generated 331705 of the 331705 1-4 parameter combinations 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: Excluding 3 bonded neighbours molecule type 'methane' 53: 53: NOTE 1 [file spc_and_methane.top, line 33]: 53: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 53: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 53: the time step of 2.0e-03 ps. 53: Maybe you forgot to change the constraints mdp option. 53: 53: Number of degrees of freedom in T-Coupling group System is 18.00 53: 53: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 2 notes 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 53: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 53: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: This run will generate roughly 0 Mb of data 53: [ OK ] GmxApiTest.BuildApiWorkflowImpl (542 ms) 53: [ RUN ] GmxApiTest.CreateApiWorkflow 53: Setting the LD random seed to -73925901 53: Generated 331705 of the 331705 non-bonded parameter combinations 53: Generating 1-4 interactions: fudge = 0.5 53: Generated 331705 of the 331705 1-4 parameter combinations 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: Excluding 3 bonded neighbours molecule type 'methane' 53: 53: NOTE 1 [file spc_and_methane.top, line 33]: 53: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 53: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 53: the time step of 2.0e-03 ps. 53: Maybe you forgot to change the constraints mdp option. 53: 53: Number of degrees of freedom in T-Coupling group System is 18.00 53: 53: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 2 notes 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 53: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 53: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: This run will generate roughly 0 Mb of data 53: [ OK ] GmxApiTest.CreateApiWorkflow (571 ms) 53: [----------] 2 tests from GmxApiTest (1113 ms total) 53: 53: [----------] Global test environment tear-down 53: [==========] 2 tests from 1 test case ran. (1113 ms total) 53: [ PASSED ] 2 tests. 53/54 Test #53: GmxapiInternalInterfaceTests ........ Passed 1.13 sec test 54 Start 54: GmxapiInternalsMpiTests 54: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic/bin/workflow-details-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic/Testing/Temporary/GmxapiInternalsMpiTests.xml" 54: Test timeout computed to be: 600 54: [==========] Running 2 tests from 1 test case. 54: [----------] Global test environment set-up. 54: [----------] 2 tests from GmxApiTest 54: [ RUN ] GmxApiTest.BuildApiWorkflowImpl 54: Setting the LD random seed to -273726721 54: Generated 331705 of the 331705 non-bonded parameter combinations 54: Generating 1-4 interactions: fudge = 0.5 54: Generated 331705 of the 331705 1-4 parameter combinations 54: Excluding 2 bonded neighbours molecule type 'SOL' 54: Excluding 3 bonded neighbours molecule type 'methane' 54: 54: NOTE 1 [file spc_and_methane.top, line 33]: 54: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 54: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 54: the time step of 2.0e-03 ps. 54: Maybe you forgot to change the constraints mdp option. 54: 54: Number of degrees of freedom in T-Coupling group System is 18.00 54: 54: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 54: You are using a plain Coulomb cut-off, which might produce artifacts. 54: You might want to consider using PME electrostatics. 54: 54: 54: 54: There were 2 notes 54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 54: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 54: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 54: Note that mdrun will redetermine rlist based on the actual pair-list setup 54: This run will generate roughly 0 Mb of data 54: [ OK ] GmxApiTest.BuildApiWorkflowImpl (570 ms) 54: [ RUN ] GmxApiTest.CreateApiWorkflow 54: Setting the LD random seed to -1082130433 54: Generated 331705 of the 331705 non-bonded parameter combinations 54: Generating 1-4 interactions: fudge = 0.5 54: Generated 331705 of the 331705 1-4 parameter combinations 54: Excluding 2 bonded neighbours molecule type 'SOL' 54: Excluding 3 bonded neighbours molecule type 'methane' 54: 54: NOTE 1 [file spc_and_methane.top, line 33]: 54: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 54: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 54: the time step of 2.0e-03 ps. 54: Maybe you forgot to change the constraints mdp option. 54: 54: Number of degrees of freedom in T-Coupling group System is 18.00 54: 54: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 54: You are using a plain Coulomb cut-off, which might produce artifacts. 54: You might want to consider using PME electrostatics. 54: 54: 54: 54: There were 2 notes 54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 54: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 54: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 54: Note that mdrun will redetermine rlist based on the actual pair-list setup 54: This run will generate roughly 0 Mb of data 54: [ OK ] GmxApiTest.CreateApiWorkflow (484 ms) 54: [----------] 2 tests from GmxApiTest (1054 ms total) 54: 54: [----------] Global test environment tear-down 54: [==========] 2 tests from 1 test case ran. (1054 ms total) 54: [ PASSED ] 2 tests. 54/54 Test #54: GmxapiInternalsMpiTests ............. Passed 1.07 sec 100% tests passed, 0 tests failed out of 54 Label Time Summary: GTest = 114.35 sec*proc (54 tests) IntegrationTest = 33.94 sec*proc (12 tests) MpiTest = 67.23 sec*proc (8 tests) SlowTest = 57.11 sec*proc (2 tests) UnitTest = 23.29 sec*proc (40 tests) Total Test time (real) = 114.41 sec /usr/bin/make -j4 -C build/basic-dp tests make[1]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/cmake -S/build/gromacs-5atmZb/gromacs-2020.6 -B/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 tests make[2]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/cmake -S/build/gromacs-5atmZb/gromacs-2020.6 -B/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/CMakeFiles 96 /usr/bin/make -f 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'/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 0%] Built target scanner make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend [ 3%] Built target thread_mpi [ 1%] Built target lmfit_objlib /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/linearalgebra /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp 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/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build'. make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build [ 3%] Built target linearalgebra [ 4%] Built target tng_io_obj /usr/bin/make -f src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build.make src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/depend /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/external/googletest/googlemock/gtest /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 4%] Built target vmddlopen make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= [ 5%] Built target modularsimulator make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' Scanning dependencies of target gtest make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build.make src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/external/googletest/googlemock/gtest && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_CREATE_SHARED_LIBRARY=1 -Dgtest_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wshadow -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=c++14 -o CMakeFiles/gtest.dir/src/gtest-all.cc.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/src/gtest-all.cc [ 5%] Built target mdrun_objlib make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 65%] Built target libgromacs /usr/bin/make -f src/api/cpp/CMakeFiles/gmxapi.dir/build.make src/api/cpp/CMakeFiles/gmxapi.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/CMakeFiles/gmxapi.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/api/cpp/CMakeFiles/gmxapi.dir/build.make src/api/cpp/CMakeFiles/gmxapi.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' make[4]: Nothing to be done for 'src/api/cpp/CMakeFiles/gmxapi.dir/build'. make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 66%] Built target gmxapi cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/external/googletest/googlemock/gtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgtest.so -o ../../../../../lib/libgtest.so CMakeFiles/gtest.dir/src/gtest-all.cc.o -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 66%] Built target gtest /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/external/googletest/googlemock /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/external/googletest/googlemock/CMakeFiles/gmock.dir/DependInfo.cmake --color= Scanning dependencies of target gmock make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/external/googletest/googlemock && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -D_GNU_SOURCE=1 -Dgmock_EXPORTS -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wshadow -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated-copy -std=c++14 -o CMakeFiles/gmock.dir/src/gmock-all.cc.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/src/gmock-all.cc cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmock.so -o ../../../../lib/libgmock.so CMakeFiles/gmock.dir/src/gmock-all.cc.o -lpthread ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 66%] Built target gmock /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/testutils /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/testutils /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/testutils/CMakeFiles/testutils.dir/DependInfo.cmake --color= Scanning dependencies of target testutils make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/cmdlinetest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/cmdlinetest.cpp cd 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-isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/xvgtest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/xvgtest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tinyxml2/tinyxml2.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/testutils && /usr/bin/cmake -P CMakeFiles/testutils.dir/cmake_clean_target.cmake cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/testutils && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils.dir/link.txt --verbose=1 /usr/bin/ar qc ../../lib/libtestutils.a CMakeFiles/testutils.dir/cmdlinetest.cpp.o CMakeFiles/testutils.dir/conftest.cpp.o CMakeFiles/testutils.dir/filematchers.cpp.o CMakeFiles/testutils.dir/interactivetest.cpp.o CMakeFiles/testutils.dir/loggertest.cpp.o CMakeFiles/testutils.dir/mpi_printer.cpp.o CMakeFiles/testutils.dir/mpitest.cpp.o CMakeFiles/testutils.dir/refdata.cpp.o CMakeFiles/testutils.dir/refdata_xml.cpp.o CMakeFiles/testutils.dir/simulationdatabase.cpp.o CMakeFiles/testutils.dir/stdiohelper.cpp.o CMakeFiles/testutils.dir/stringtest.cpp.o CMakeFiles/testutils.dir/testasserts.cpp.o CMakeFiles/testutils.dir/testfilemanager.cpp.o CMakeFiles/testutils.dir/testfileredirector.cpp.o CMakeFiles/testutils.dir/testinit.cpp.o CMakeFiles/testutils.dir/testmatchers.cpp.o CMakeFiles/testutils.dir/testoptions.cpp.o CMakeFiles/testutils.dir/textblockmatchers.cpp.o CMakeFiles/testutils.dir/tprfilegenerator.cpp.o CMakeFiles/testutils.dir/xvgtest.cpp.o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o /usr/bin/ranlib ../../lib/libtestutils.a make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 68%] Built target testutils /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/depend /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/depend /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/depend /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/testutils/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/DependInfo.cmake --color= cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/testutils/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/testutils/tests/CMakeFiles/testutils-test.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/DependInfo.cmake --color= Scanning dependencies of target testutils-mpi-test Scanning dependencies of target utility-mpi-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f 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-isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/tests/mpitest.cpp Scanning dependencies of target testutils-test make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" 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'/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/interactivetest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/tests/interactivetest.cpp Scanning dependencies of target mdrun_test_infrastructure make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/energyreader.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/energycomparison.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.5.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../lib/libgtest.so -lpthread cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 68%] Built target testutils-mpi-test /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 68%] Built target utility-mpi-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/moduletest.cpp Scanning dependencies of target utility-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/alignedallocator.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/tests/refdata_tests.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/tests/testasserts_tests.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/mdmodulenotification.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/mdmodulenotification.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/terminationhelper.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/trajectorycomparison.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/trajectoryreader.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/tests/xvgtest_tests.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/arrayref.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/bitmask32.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-test.dir/interactivetest.cpp.o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.5.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 69%] Built target testutils-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/bitmask64.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/mdmodulenotification.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o /usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 70%] Built target mdrun_test_infrastructure cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/bitmask128.cpp /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdlib-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/calc_verletbuf.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/cstringutil.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/constr.cpp /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/applied_forces/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/applied_forces/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake --color= Scanning dependencies of target applied_forces-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfitting.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/applied_forces/tests/densityfitting.cpp /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/onlinehelp/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/onlinehelp/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color= Scanning dependencies of target onlinehelp-test-shared make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/onlinehelp/tests/mock_helptopic.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfittingoptions.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/applied_forces/tests/densityfittingoptions.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o /usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 70%] Built target onlinehelp-test-shared cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/applied_forces/tests/densityfittingamplitudelookup.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/constrtestdata.cpp /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/domdec/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/domdec/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color= Scanning dependencies of target domdec-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/domdec/tests/hashedmap.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/constrtestrunners.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/domdec/tests/localatomsetmanager.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/applied_forces/tests/electricfield.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/ebin.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/energyoutput.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/domdec-test.dir/hashedmap.cpp.o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 70%] Built target domdec-test /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/ewald/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color= Scanning dependencies of target ewald-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/tests/pmebsplinetest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/applied_forces-test.dir/densityfitting.cpp.o CMakeFiles/applied_forces-test.dir/densityfittingoptions.cpp.o CMakeFiles/applied_forces-test.dir/densityfittingamplitudelookup.cpp.o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 71%] Built target applied_forces-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/tests/pmegathertest.cpp /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fft/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/fft/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color= Scanning dependencies of target fft-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fft-test.dir/fft.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fft/tests/fft.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/expanded.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fft-test.dir/fft.cpp.o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 71%] Built target fft-test /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gpu_utils/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gpu_utils/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color= Scanning dependencies of target gpu_utils-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/gputest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gpu_utils/tests/gputest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/tests/pmesolvetest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gpu_utils/tests/clfftinitializer.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/leapfrog.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gpu_utils/tests/hostallocator.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/defaultinitializationallocator.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/leapfrogtestdata.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/enumerationhelpers.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/tests/pmesplinespreadtest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/fixedcapacityvector.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/settle.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/inmemoryserializer.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/keyvaluetreeserializer.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/tests/pmetestcommon.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/settletestdata.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/settletestrunners.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/tests/testhardwarecontexts.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/shake.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/keyvaluetreetransform.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gpu_utils/tests/devicetransfers.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 72%] Built target ewald-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/logger.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/logger.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gpu_utils-test.dir/gputest.cpp.o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 72%] Built target gpu_utils-test /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/hardware/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/hardware/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color= Scanning dependencies of target hardware-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/hardware/tests/hardwaretopology.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/simulationsignal.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/updategroups.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/mutex.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/updategroupscog.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/path.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/path.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 73%] Built target hardware-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/physicalnodecommunicator.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/constr.cpp.o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o CMakeFiles/mdlib-test.dir/ebin.cpp.o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o CMakeFiles/mdlib-test.dir/expanded.cpp.o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o CMakeFiles/mdlib-test.dir/settle.cpp.o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o CMakeFiles/mdlib-test.dir/shake.cpp.o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o CMakeFiles/mdlib-test.dir/updategroups.cpp.o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 75%] Built target mdlib-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/stringutil.cpp /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color= cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/textreader.cpp Scanning dependencies of target math-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/arrayrefwithpadding.cpp /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdrunutility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-test-shared make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o /usr/bin/ranlib ../../../../lib/libmdrunutility-test-shared.a make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 75%] Built target mdrunutility-test-shared /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdspan/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdspan/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdspan-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdspan/tests/accessor_policy.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/coordinatetransformation.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/extents.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdspan/tests/extents.cpp /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/onlinehelp/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/onlinehelp/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color= Scanning dependencies of target onlinehelp-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/onlinehelp/tests/helpformat.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/textwriter.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/extensions.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdspan/tests/extensions.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/onlinehelp/tests/helpmanager.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/typetraits.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/densityfit.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/densityfit.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/layouts.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdspan/tests/layouts.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-test.dir/alignedallocator.cpp.o CMakeFiles/utility-test.dir/arrayref.cpp.o CMakeFiles/utility-test.dir/bitmask32.cpp.o CMakeFiles/utility-test.dir/bitmask64.cpp.o CMakeFiles/utility-test.dir/bitmask128.cpp.o CMakeFiles/utility-test.dir/cstringutil.cpp.o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/stringutil.cpp.o CMakeFiles/utility-test.dir/textreader.cpp.o CMakeFiles/utility-test.dir/textwriter.cpp.o CMakeFiles/utility-test.dir/typetraits.cpp.o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 76%] Built target utility-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/mdspan.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdspan/tests/mdspan.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/onlinehelp/tests/helpwritercontext.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 77%] Built target onlinehelp-test /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/options/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color= Scanning dependencies of target options-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/options/tests/abstractoptionstorage.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/dofit.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/dofit.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/exponentialmovingaverage.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/options/tests/filenameoption.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/functions.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/functions.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/gausstransform.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/gausstransform.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/options/tests/filenameoptionmanager.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/densityfittingforce.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o CMakeFiles/mdspan-test.dir/extents.cpp.o CMakeFiles/mdspan-test.dir/extensions.cpp.o CMakeFiles/mdspan-test.dir/layouts.cpp.o CMakeFiles/mdspan-test.dir/mdspan.cpp.o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 78%] Built target mdspan-test /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/pbcutil/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/pbcutil/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake --color= Scanning dependencies of target pbcutil-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/pbcutil/tests/pbc.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/pbcutil/tests/pbcenums.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/invertmatrix.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/matrix.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/matrix.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pbcutil-test.dir/pbc.cpp.o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 78%] Built target pbcutil-test /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/random/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color= Scanning dependencies of target random-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/random/tests/exponentialdistribution.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/multidimarray.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/option.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/options/tests/option.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/options/tests/optionsassigner.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/options/tests/repeatingsection.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/random/tests/gammadistribution.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/paddedvector.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/random/tests/normaldistribution.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/seed.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/random/tests/seed.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/random/tests/tabulatednormaldistribution.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/threefry.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/random/tests/threefry.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/options/tests/timeunitmanager.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/random/tests/uniformintdistribution.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/options/tests/treesupport.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/random/tests/uniformrealdistribution.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/restraint/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/restraint/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color= Scanning dependencies of target restraintpotential-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/restraint/tests/manager.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/random-test.dir/exponentialdistribution.cpp.o CMakeFiles/random-test.dir/gammadistribution.cpp.o CMakeFiles/random-test.dir/normaldistribution.cpp.o CMakeFiles/random-test.dir/seed.cpp.o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o CMakeFiles/random-test.dir/threefry.cpp.o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/restraintpotential-test.dir/manager.cpp.o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 79%] Built target random-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/vectypes.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 79%] Built target restraintpotential-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/tables/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/tables/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color= Scanning dependencies of target table-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/tables/tests/splinetable.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1 cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o CMakeFiles/options-test.dir/filenameoption.cpp.o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o CMakeFiles/options-test.dir/option.cpp.o CMakeFiles/options-test.dir/optionsassigner.cpp.o CMakeFiles/options-test.dir/repeatingsection.cpp.o CMakeFiles/options-test.dir/timeunitmanager.cpp.o CMakeFiles/options-test.dir/treesupport.cpp.o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 80%] Built target options-test /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/taskassignment/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/taskassignment/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color= Scanning dependencies of target taskassignment-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/taskassignment/tests/usergpuids.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/topology/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/topology/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake --color= Scanning dependencies of target topology-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/topology/tests/exclusionblocks.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o CMakeFiles/math-test.dir/densityfit.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/gausstransform.cpp.o CMakeFiles/math-test.dir/densityfittingforce.cpp.o CMakeFiles/math-test.dir/invertmatrix.cpp.o CMakeFiles/math-test.dir/matrix.cpp.o CMakeFiles/math-test.dir/multidimarray.cpp.o CMakeFiles/math-test.dir/paddedvector.cpp.o CMakeFiles/math-test.dir/vectypes.cpp.o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/topology/tests/mtop.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 81%] Built target math-test /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/pulling/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/pulling/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color= Scanning dependencies of target pull-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pull-test.dir/pull.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/pulling/tests/pull.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/topology/tests/symtab.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 81%] Built target taskassignment-test /usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/awh/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/awh/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color= Scanning dependencies of target awh-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/bias.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/awh/tests/bias.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pull-test.dir/pull.cpp.o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 81%] Built target pull-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color= Scanning dependencies of target simd-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/bootstrap_loadstore.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/topology-test.dir/exclusionblocks.cpp.o CMakeFiles/topology-test.dir/mtop.cpp.o CMakeFiles/topology-test.dir/symtab.cpp.o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 81%] Built target topology-test /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/compat/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/compat/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color= Scanning dependencies of target compat-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-unused-member-function -o CMakeFiles/compat-test.dir/optional.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/compat/tests/optional.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/base.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/base.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/table-test.dir/splinetable.cpp.o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 81%] Built target table-test /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxana/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake --color= Scanning dependencies of target gmxana-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxana/tests/entropy.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/awh/tests/biasstate.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxana/tests/gmx_traj.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd_floatingpoint.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/grid.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/awh/tests/grid.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxana/tests/gmx_mindist.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxana/tests/gmx_msd.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/grid.cpp.o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/awh-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 81%] Built target awh-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd_floatingpoint_util.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/compat/tests/pointers.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/string_view.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/compat/tests/string_view.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxana-test.dir/entropy.cpp.o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 82%] Built target gmxana-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake --color= Scanning dependencies of target pdb2gmx3-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=1 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake --color= Scanning dependencies of target pdb2gmx2-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd_vector_operations.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd_math.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=1 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx3-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 82%] Built target pdb2gmx3-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake --color= Scanning dependencies of target pdb2gmx1-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx2-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 83%] Built target pdb2gmx2-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake --color= Scanning dependencies of target gmxpreprocess-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/editconf.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/compat-test.dir/optional.cpp.o CMakeFiles/compat-test.dir/pointers.cpp.o CMakeFiles/compat-test.dir/string_view.cpp.o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 83%] Built target compat-test /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/correlationfunctions/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/correlationfunctions/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake --color= Scanning dependencies of target correlations-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/autocorr.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/correlationfunctions/tests/autocorr.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/genconf.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/genion.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/correlationfunctions/tests/correlationdataset.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 83%] Built target pdb2gmx1-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/expfit.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/correlationfunctions/tests/expfit.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/genrestr.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd_memory.cpp /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/analysisdata/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake --color= Scanning dependencies of target analysisdata-test-shared make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/analysisdata/tests/datatest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/correlations-test.dir/autocorr.cpp.o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o CMakeFiles/correlations-test.dir/expfit.cpp.o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 84%] Built target correlations-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/analysisdata/tests/mock_datamodule.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/insert_molecules.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd_integer.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/readir.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/solvate.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG 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-ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd4_floatingpoint.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd4_vector_operations.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd4_math.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 85%] Built target gmxpreprocess-test /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/coordinateio/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/DependInfo.cmake --color= Scanning dependencies of target coordinateio-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/builder.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/coordinateio/tests/builder.cpp /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/energyanalysis/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/energyanalysis/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake --color= Scanning dependencies of target energyanalysis-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/energyanalysis/tests/legacyenergy.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/scalar.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libanalysisdata-test-shared.a CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o /usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 85%] Built target analysisdata-test-shared cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/scalar_util.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 85%] Built target energyanalysis-test /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/tools/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake --color= Scanning dependencies of target tool-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/dump.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/tools/tests/dump.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/coordinateio/tests/outputadaptercontainer.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/tools/tests/report_methods.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/scalar_math.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/coordinateio/tests/outputadapters.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/requirements.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/coordinateio/tests/requirements.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/trjconv.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/tools/tests/trjconv.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/coordinateio/tests/setatoms.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/base.cpp.o CMakeFiles/simd-test.dir/simd.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4_math.cpp.o CMakeFiles/simd-test.dir/scalar.cpp.o CMakeFiles/simd-test.dir/scalar_util.cpp.o CMakeFiles/simd-test.dir/scalar_math.cpp.o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 87%] Built target simd-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/coordinateio/tests/setbothtime.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/tool-test.dir/dump.cpp.o CMakeFiles/tool-test.dir/report_methods.cpp.o CMakeFiles/tool-test.dir/trjconv.cpp.o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 88%] Built target tool-test /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color= Scanning dependencies of target fileio-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio/tests/confio.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/coordinateio/tests/setstarttime.cpp /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/selection/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake --color= Scanning dependencies of target selection-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/tests/indexutil.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/coordinateio/tests/settimestep.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio/tests/filemd5.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio/tests/mrcserializer.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/coordinateio/tests/testmodule.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio/tests/mrcdensitymap.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/tests/nbsearch.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/coordinateio-test.dir/builder.cpp.o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o CMakeFiles/coordinateio-test.dir/requirements.cpp.o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio/tests/mrcdensitymapheader.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 89%] Built target coordinateio-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio/tests/readinp.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/tests/poscalc.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio/tests/fileioxdrserializer.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/tests/selectioncollection.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio/tests/tngio.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun-modules-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/densityfittingmodule.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/tests/selectionoption.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 90%] Built target fileio-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/tests/toputils.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/interactiveMD.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/mimic.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun-tpi-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/tpitest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-modules-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 90%] Built target mdrun-modules-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/dispersion_correction.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/dispersion_correction.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-tpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 90%] Built target mdrun-tpi-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun-output-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/compressed_x_output.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/orires.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/orires.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/pmetest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/pmetest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/simulator.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/simulator.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/helpwriting.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/selection-test.dir/indexutil.cpp.o CMakeFiles/selection-test.dir/nbsearch.cpp.o CMakeFiles/selection-test.dir/poscalc.cpp.o CMakeFiles/selection-test.dir/selectioncollection.cpp.o CMakeFiles/selection-test.dir/selectionoption.cpp.o CMakeFiles/selection-test.dir/toputils.cpp.o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 90%] Built target selection-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/outputfiles.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/swapcoords.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/trajectory_writing.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun-non-integrator-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/minimize.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun-mpi-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/domain_decomposition.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-test.dir/dispersion_correction.cpp.o CMakeFiles/mdrun-test.dir/orires.cpp.o CMakeFiles/mdrun-test.dir/pmetest.cpp.o CMakeFiles/mdrun-test.dir/simulator.cpp.o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 91%] Built target mdrun-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun-io-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/exactcontinuation.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/minimize.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 92%] Built target mdrun-output-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun-mpi-coordination-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/periodicactions.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/nonbonded_bench.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/normalmodes.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/grompp.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/mimic.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/initialconstraints.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-coordination-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-coordination-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 92%] Built target mdrun-mpi-coordination-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/termination.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/termination.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/multisim.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/multisimtest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/rerun.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/simple_mdrun.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-io-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o CMakeFiles/mdrun-io-test.dir/termination.cpp.o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-io-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/pmetest.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 93%] Built target mdrun-io-test /usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target gmxapi-mpi-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests/restraint.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests/status.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/tests/replicaexchange.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests/system.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests/version.cpp /usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/DependInfo.cmake --color= Scanning dependencies of target gmxapi-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/restraint.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests/restraint.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 93%] Built target mdrun-non-integrator-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp /usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/workflow/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/workflow/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target workflow-details-mpi-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-mpi-test.dir/workflow.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/workflow/tests/workflow.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 94%] Built target mdrun-mpi-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/status.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests/status.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests/runner.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests/stopsignaler.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/system.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests/system.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-mpi-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/version.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests/version.cpp /usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/workflow/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/workflow/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/DependInfo.cmake --color= Scanning dependencies of target workflow-details-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-test.dir/workflow.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/workflow/tests/workflow.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/workflow-details-mpi-test.dir/workflow.cpp.o CMakeFiles/workflow-details-mpi-test.dir/__/__/__/__/testutils/unittest_main.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-mpi-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi_d.so.0.1.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../../lib/libgmock.so ../../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 94%] Built target workflow-details-mpi-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o CMakeFiles/gmxapi-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi_d.so.0.1.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/commandline/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color= [ 94%] Built target gmxapi-mpi-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/runner.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests/runner.cpp Scanning dependencies of target commandline-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests -I/build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp/tests/stopsignaler.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/workflow-details-test.dir/workflow.cpp.o CMakeFiles/workflow-details-test.dir/__/__/__/__/testutils/unittest_main.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi_d.so.0.1.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../../lib/libgmock.so ../../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 95%] Built target workflow-details-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdrunutility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-mpi-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdrunutility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdrunutility/tests/threadaffinity.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxapi-test.dir/restraint.cpp.o CMakeFiles/gmxapi-test.dir/status.cpp.o CMakeFiles/gmxapi-test.dir/system.cpp.o CMakeFiles/gmxapi-test.dir/version.cpp.o CMakeFiles/gmxapi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/gmxapi-test.dir/runner.cpp.o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi_d.so.0.1.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 96%] Built target gmxapi-test /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/analysisdata/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake --color= Scanning dependencies of target analysisdata-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/analysisdata/tests/analysisdata.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 96%] Built target mdrunutility-mpi-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/analysisdata/tests/arraydata.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 96%] Built target mdrunutility-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/analysisdata/tests/average.cpp /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake --color= Scanning dependencies of target trajectoryanalysis-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/moduletest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/analysisdata/tests/histogram.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/analysisdata/tests/lifetime.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/angle.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/tests/cmdlineparser.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o CMakeFiles/analysisdata-test.dir/average.cpp.o CMakeFiles/analysisdata-test.dir/histogram.cpp.o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 96%] Built target analysisdata-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 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/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/convert_trj.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG 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/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 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-ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/unionfind.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o CMakeFiles/commandline-test.dir/filenm.cpp.o CMakeFiles/commandline-test.dir/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 97%] Built target commandline-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [100%] Built target trajectoryanalysis-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/CMakeFiles/tests.dir/DependInfo.cmake --color= Scanning dependencies of target tests make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [100%] Built target tests make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/cmake -E cmake_progress_start /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/CMakeFiles 0 make[2]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' make[1]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' (cd build/basic-dp; LD_LIBRARY_PATH=/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/lib ctest -V || dpkg-architecture -i hurd-i386 || dpkg-architecture -i i386 ) UpdateCTestConfiguration from :/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/DartConfiguration.tcl Parse Config file:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/DartConfiguration.tcl UpdateCTestConfiguration from :/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/DartConfiguration.tcl Parse Config file:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/DartConfiguration.tcl Test project /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: TestUtilsUnitTests 1: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/testutils-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/TestUtilsUnitTests.xml" 1: Test timeout computed to be: 30 1: [==========] Running 59 tests from 5 test cases. 1: [----------] Global test environment set-up. 1: [----------] 10 tests from InteractiveTestHelperTest 1: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 1: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (36 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (1 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 1: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 1: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 1: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) 1: [----------] 10 tests from InteractiveTestHelperTest (39 ms total) 1: 1: [----------] 34 tests from ReferenceDataTest 1: [ RUN ] ReferenceDataTest.HandlesSimpleData 1: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 1: [ OK ] ReferenceDataTest.HandlesFloatingPointData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 1: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesStringBlockData 1: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesVectorData 1: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceData 1: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 1: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesIncorrectData 1: [ OK ] ReferenceDataTest.HandlesIncorrectData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 1: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMissingData 1: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedData 1: [ OK ] ReferenceDataTest.HandlesUncheckedData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesAnys 1: [ OK ] ReferenceDataTest.HandlesAnys (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 1: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue 1: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType 1: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 1: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 1: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 1: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 1: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 1: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 1: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 1: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 1: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 1: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesReadingValues 1: [ OK ] ReferenceDataTest.HandlesReadingValues (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (0 ms) 1: [----------] 34 tests from ReferenceDataTest (8 ms total) 1: 1: [----------] 7 tests from FloatingPointDifferenceTest 1: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 1: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 1: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 1: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 1: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 1: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 1: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 1: 1: [----------] 4 tests from FloatingPointToleranceTest 1: [ RUN ] FloatingPointToleranceTest.UlpTolerance 1: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 1: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 1: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 1: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 1: 1: [----------] 4 tests from XvgTests 1: [ RUN ] XvgTests.CreateFile 1: [ OK ] XvgTests.CreateFile (1 ms) 1: [ RUN ] XvgTests.CheckMissing 1: [ OK ] XvgTests.CheckMissing (0 ms) 1: [ RUN ] XvgTests.CheckExtra 1: [ OK ] XvgTests.CheckExtra (1 ms) 1: [ RUN ] XvgTests.ReadIncorrect 1: [ OK ] XvgTests.ReadIncorrect (0 ms) 1: [----------] 4 tests from XvgTests (2 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 59 tests from 5 test cases ran. (49 ms total) 1: [ PASSED ] 59 tests. 1/54 Test #1: TestUtilsUnitTests .................. Passed 0.06 sec test 2 Start 2: TestUtilsMpiUnitTests 2: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/TestUtilsMpiUnitTests.xml" 2: Test timeout computed to be: 30 2: [==========] Running 1 test from 1 test case. 2: [----------] Global test environment set-up. 2: [----------] 1 test from MpiSelfTest 2: [ RUN ] MpiSelfTest.Runs 2: [ OK ] MpiSelfTest.Runs (1 ms) 2: [----------] 1 test from MpiSelfTest (1 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 1 test from 1 test case ran. (1 ms total) 2: [ PASSED ] 1 test. 2/54 Test #2: TestUtilsMpiUnitTests ............... Passed 0.01 sec test 3 Start 3: UtilityUnitTests 3: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/utility-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/UtilityUnitTests.xml" 3: Test timeout computed to be: 30 3: [==========] Running 347 tests from 56 test cases. 3: [----------] Global test environment set-up. 3: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 3: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/0.Move 3: [ OK ] AllocatorTest/0.Move (0 ms) 3: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/0 (0 ms total) 3: 3: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 3: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (1 ms) 3: [ RUN ] AllocatorTest/1.Move 3: [ OK ] AllocatorTest/1.Move (0 ms) 3: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/1 (1 ms total) 3: 3: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 3: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/2.Move 3: [ OK ] AllocatorTest/2.Move (0 ms) 3: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/2 (0 ms total) 3: 3: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 3: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/3.Move 3: [ OK ] AllocatorTest/3.Move (0 ms) 3: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/3 (0 ms total) 3: 3: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 3: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/4.Move 3: [ OK ] AllocatorTest/4.Move (0 ms) 3: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/4 (0 ms total) 3: 3: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 3: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/5.Move 3: [ OK ] AllocatorTest/5.Move (0 ms) 3: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/5 (1 ms total) 3: 3: [----------] 1 test from AllocatorUntypedTest 3: [ RUN ] AllocatorUntypedTest.Comparison 3: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 3: [----------] 1 test from AllocatorUntypedTest (0 ms total) 3: 3: [----------] 1 test from EmptyArrayRefTest 3: [ RUN ] EmptyArrayRefTest.IsEmpty 3: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 3: [----------] 1 test from EmptyArrayRefTest (0 ms total) 3: 3: [----------] 1 test from EmptyConstArrayRefTest 3: [ RUN ] EmptyConstArrayRefTest.IsEmpty 3: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 3: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 3: 3: [----------] 2 tests from CStringUtilityTest 3: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison 3: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) 3: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength 3: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms) 3: [----------] 2 tests from CStringUtilityTest (0 ms total) 3: 3: [----------] 2 tests from DefaultInitializationAllocator 3: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization 3: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) 3: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization 3: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) 3: [----------] 2 tests from DefaultInitializationAllocator (0 ms total) 3: 3: [----------] 4 tests from EnumerationHelpersTest 3: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks 3: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (1 ms) 3: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks 3: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) 3: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe 3: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) 3: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks 3: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) 3: [----------] 4 tests from EnumerationHelpersTest (1 ms total) 3: 3: [----------] 9 tests from FixedCapacityVectorTest 3: [ RUN ] FixedCapacityVectorTest.IsEmpty 3: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) 3: [ RUN ] FixedCapacityVectorTest.PushWorks 3: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.PopWorks 3: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.ClearWorks 3: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks 3: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.AtThrows 3: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms) 3: [ RUN ] FixedCapacityVectorTest.IteratorWorks 3: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks 3: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks 3: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) 3: [----------] 9 tests from FixedCapacityVectorTest (0 ms total) 3: 3: [----------] 5 tests from InMemorySerializerTest 3: [ RUN ] InMemorySerializerTest.Roundtrip 3: [ OK ] InMemorySerializerTest.Roundtrip (0 ms) 3: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap 3: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) 3: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap 3: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) 3: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap 3: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms) 3: [ RUN ] InMemorySerializerTest.SizeIsCorrect 3: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) 3: [----------] 5 tests from InMemorySerializerTest (0 ms total) 3: 3: [----------] 4 tests from KeyValueTreeSerializerTest 3: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 3: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms) 3: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 3: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) 3: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 3: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms) 3: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 3: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (1 ms) 3: [----------] 4 tests from KeyValueTreeSerializerTest (1 ms total) 3: 3: [----------] 6 tests from TreeValueTransformTest 3: [ RUN ] TreeValueTransformTest.SimpleTransforms 3: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) 3: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 3: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) 3: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 3: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms) 3: [ RUN ] TreeValueTransformTest.ObjectFromString 3: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) 3: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 3: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) 3: [ RUN ] TreeValueTransformTest.ScopedTransformRules 3: [ OK ] TreeValueTransformTest.ScopedTransformRules (1 ms) 3: [----------] 6 tests from TreeValueTransformTest (1 ms total) 3: 3: [----------] 1 test from TreeValueTransformErrorTest 3: [ RUN ] TreeValueTransformErrorTest.ConversionError 3: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms) 3: [----------] 1 test from TreeValueTransformErrorTest (0 ms total) 3: 3: [----------] 7 tests from LoggerTest 3: [ RUN ] LoggerTest.EmptyLoggerWorks 3: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 3: [ RUN ] LoggerTest.LogsToStream 3: [ OK ] LoggerTest.LogsToStream (0 ms) 3: [ RUN ] LoggerTest.LogsToFile 3: [ OK ] LoggerTest.LogsToFile (0 ms) 3: [ RUN ] LoggerTest.LevelFilteringWorks 3: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 3: [ RUN ] LoggerTest.LogsToMultipleStreams 3: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 3: [ RUN ] LoggerTest.LogsToMultipleFiles 3: [ OK ] LoggerTest.LogsToMultipleFiles (1 ms) 3: [ RUN ] LoggerTest.LogsToStreamAndFile 3: [ OK ] LoggerTest.LogsToStreamAndFile (0 ms) 3: [----------] 7 tests from LoggerTest (1 ms total) 3: 3: [----------] 4 tests from MutexBasicTest 3: [ RUN ] MutexBasicTest.CanBeMade 3: [ OK ] MutexBasicTest.CanBeMade (0 ms) 3: [ RUN ] MutexBasicTest.CanBeLocked 3: [ OK ] MutexBasicTest.CanBeLocked (0 ms) 3: [ RUN ] MutexBasicTest.CanBeTryLocked 3: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms) 3: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard 3: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms) 3: [----------] 4 tests from MutexBasicTest (0 ms total) 3: 3: [----------] 3 tests from MutexTaskTest 3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock 3: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (1 ms) 3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread 3: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (0 ms) 3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread 3: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms) 3: [----------] 3 tests from MutexTaskTest (1 ms total) 3: 3: [----------] 2 tests from PathTest 3: [ RUN ] PathTest.StripSourcePrefixWorks 3: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 3: [ RUN ] PathTest.SearchOperationsWork 3: [ OK ] PathTest.SearchOperationsWork (0 ms) 3: [----------] 2 tests from PathTest (0 ms total) 3: 3: [----------] 2 tests from PhysicalNodeCommunicatorTest 3: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 3: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 3: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 3: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 3: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 3: 3: [----------] 9 tests from StringUtilityTest 3: [ RUN ] StringUtilityTest.StartsWith 3: [ OK ] StringUtilityTest.StartsWith (0 ms) 3: [ RUN ] StringUtilityTest.EndsWith 3: [ OK ] StringUtilityTest.EndsWith (0 ms) 3: [ RUN ] StringUtilityTest.StripSuffixIfPresent 3: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 3: [ RUN ] StringUtilityTest.StripString 3: [ OK ] StringUtilityTest.StripString (0 ms) 3: [ RUN ] StringUtilityTest.SplitString 3: [ OK ] StringUtilityTest.SplitString (0 ms) 3: [ RUN ] StringUtilityTest.SplitDelimitedString 3: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 3: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 3: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (1 ms) 3: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive 3: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) 3: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength 3: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) 3: [----------] 9 tests from StringUtilityTest (1 ms total) 3: 3: [----------] 2 tests from FormatStringTest 3: [ RUN ] FormatStringTest.HandlesBasicFormatting 3: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 3: [ RUN ] FormatStringTest.HandlesLongStrings 3: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 3: [----------] 2 tests from FormatStringTest (0 ms total) 3: 3: [----------] 1 test from StringFormatterTest 3: [ RUN ] StringFormatterTest.HandlesBasicFormatting 3: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 3: [----------] 1 test from StringFormatterTest (0 ms total) 3: 3: [----------] 1 test from formatAndJoinTest 3: [ RUN ] formatAndJoinTest.Works 3: [ OK ] formatAndJoinTest.Works (0 ms) 3: [----------] 1 test from formatAndJoinTest (0 ms total) 3: 3: [----------] 1 test from JoinStringsTest 3: [ RUN ] JoinStringsTest.Works 3: [ OK ] JoinStringsTest.Works (0 ms) 3: [----------] 1 test from JoinStringsTest (0 ms total) 3: 3: [----------] 6 tests from ReplaceAllTest 3: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 3: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesNoMatches 3: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 3: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 3: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 3: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 3: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 3: [----------] 6 tests from ReplaceAllTest (0 ms total) 3: 3: [----------] 10 tests from TextLineWrapperTest 3: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 3: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 3: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 3: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 3: [ RUN ] TextLineWrapperTest.WrapsCorrectly 3: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms) 3: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 3: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesIndent 3: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 3: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 3: [ OK ] TextLineWrapperTest.HandlesHangingIndent (1 ms) 3: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 3: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) 3: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 3: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) 3: [----------] 10 tests from TextLineWrapperTest (1 ms total) 3: 3: [----------] 6 tests from TextWriterTest 3: [ RUN ] TextWriterTest.WritesLines 3: [ OK ] TextWriterTest.WritesLines (0 ms) 3: [ RUN ] TextWriterTest.WritesLinesInParts 3: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 3: [ RUN ] TextWriterTest.WritesWrappedLines 3: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) 3: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 3: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 3: [ RUN ] TextWriterTest.TracksNewlines 3: [ OK ] TextWriterTest.TracksNewlines (0 ms) 3: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 3: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 3: [----------] 6 tests from TextWriterTest (0 ms total) 3: 3: [----------] 1 test from TypeTraitsTest 3: [ RUN ] TypeTraitsTest.IsIntegralConstant 3: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 3: [----------] 1 test from TypeTraitsTest (0 ms total) 3: 3: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 3: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 3: 3: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 3: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 3: 3: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 3: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (1 ms total) 3: 3: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (3 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms) 3: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (3 ms total) 3: 3: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (1 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 3: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (1 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 347 tests from 56 test cases ran. (15 ms total) 3: [ PASSED ] 347 tests. 3/54 Test #3: UtilityUnitTests .................... Passed 0.05 sec test 4 Start 4: UtilityMpiUnitTests 4: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/utility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/UtilityMpiUnitTests.xml" 4: Test timeout computed to be: 30 4: [==========] Running 2 tests from 1 test case. 4: [----------] Global test environment set-up. 4: [----------] 2 tests from PhysicalNodeCommunicatorTest 4: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 4: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (1 ms) 4: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 4: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (1 ms) 4: [----------] 2 tests from PhysicalNodeCommunicatorTest (2 ms total) 4: 4: [----------] Global test environment tear-down 4: [==========] 2 tests from 1 test case ran. (2 ms total) 4: [ PASSED ] 2 tests. 4/54 Test #4: UtilityMpiUnitTests ................. Passed 0.02 sec test 5 Start 5: MdlibUnitTest 5: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/mdlib-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/MdlibUnitTest.xml" 5: Test timeout computed to be: 30 5: [==========] Running 187 tests from 13 test cases. 5: [----------] Global test environment set-up. 5: [----------] 1 test from VerletBufferConstraintTest 5: [ RUN ] VerletBufferConstraintTest.EqualMasses 5: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 5: [----------] 1 test from VerletBufferConstraintTest (0 ms total) 5: 5: [----------] 2 tests from PrEbinTest 5: [ RUN ] PrEbinTest.HandlesAverages 5: [ OK ] PrEbinTest.HandlesAverages (0 ms) 5: [ RUN ] PrEbinTest.HandlesEmptyAverages 5: [ OK ] PrEbinTest.HandlesEmptyAverages (1 ms) 5: [----------] 2 tests from PrEbinTest (1 ms total) 5: 5: [----------] 4 tests from ShakeTest 5: [ RUN ] ShakeTest.ConstrainsOneBond 5: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) 5: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 5: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 5: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 5: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 5: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 5: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 5: [----------] 4 tests from ShakeTest (0 ms total) 5: 5: [----------] 1 test from NullSignalTest 5: [ RUN ] NullSignalTest.NullSignallerWorks 5: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 5: [----------] 1 test from NullSignalTest (0 ms total) 5: 5: [----------] 7 tests from SignalTest 5: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 5: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 5: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 5: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 5: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 5: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 5: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 5: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 5: [----------] 7 tests from SignalTest (0 ms total) 5: 5: [----------] 9 tests from UpdateGroups 5: [ RUN ] UpdateGroups.ethaneUA 5: [ OK ] UpdateGroups.ethaneUA (0 ms) 5: [ RUN ] UpdateGroups.methane 5: [ OK ] UpdateGroups.methane (0 ms) 5: [ RUN ] UpdateGroups.ethane 5: [ OK ] UpdateGroups.ethane (0 ms) 5: [ RUN ] UpdateGroups.butaneUA 5: [ OK ] UpdateGroups.butaneUA (0 ms) 5: [ RUN ] UpdateGroups.waterThreeSite 5: [ OK ] UpdateGroups.waterThreeSite (0 ms) 5: [ RUN ] UpdateGroups.waterFourSite 5: [ OK ] UpdateGroups.waterFourSite (0 ms) 5: [ RUN ] UpdateGroups.fourAtomsWithSettle 5: [ OK ] UpdateGroups.fourAtomsWithSettle (0 ms) 5: [ RUN ] UpdateGroups.waterFlexAngle 5: [ OK ] UpdateGroups.waterFlexAngle (0 ms) 5: [ RUN ] UpdateGroups.twoMoltypes 5: [ OK ] UpdateGroups.twoMoltypes (0 ms) 5: [----------] 9 tests from UpdateGroups (0 ms total) 5: 5: [----------] 1 test from UpdateGroupsCog 5: [ RUN ] UpdateGroupsCog.ComputesCogs 5: [ OK ] UpdateGroupsCog.ComputesCogs (1 ms) 5: [----------] 1 test from UpdateGroupsCog (1 ms total) 5: 5: [----------] 84 tests from WithParameters/ConstraintsTest 5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/0 5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/1 5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/2 5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/3 5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/2 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/3 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/4 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/5 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/6 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/7 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/2 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/3 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/4 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/5 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/5 (1 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/6 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/7 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/8 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/8 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/9 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/9 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/10 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/10 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/11 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/11 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/2 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/3 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/4 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/5 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/6 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/7 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/8 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/8 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/9 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/9 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/10 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/10 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/11 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/11 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/12 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/12 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/13 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/13 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/14 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/14 (1 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/15 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/15 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/0 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/1 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/2 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/3 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/4 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/5 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/6 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/7 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/8 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/8 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/9 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/9 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/10 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/10 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/11 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/11 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/12 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/12 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/13 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/13 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/14 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/14 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/15 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/15 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/16 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/16 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/17 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/17 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/18 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/18 (1 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/19 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/19 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/0 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/1 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/2 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/3 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/4 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/5 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/6 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/7 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/8 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/8 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/9 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/9 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/10 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/10 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/11 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/11 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/12 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/12 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/13 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/13 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/14 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/14 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/15 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/15 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/16 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/16 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/17 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/17 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/18 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/18 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/19 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/19 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/20 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/20 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/21 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/21 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/22 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/22 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/23 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/23 (0 ms) 5: [----------] 84 tests from WithParameters/ConstraintsTest (3 ms total) 5: 5: [----------] 11 tests from WithParameters/EnergyOutputTest 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as double precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (2 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as double precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (27 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as double precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (8 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3 5: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (0 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as double precision energy file 5: Reading energy frame 0 time 10.100 Reading energy frame 1 time 27.500 Reading energy frame 2 time 44.900 Reading energy frame 3 time 62.300 Reading energy frame 4 time 79.700 Reading energy frame 5 time 97.100 Reading energy frame 6 time 114.500 Reading energy frame 7 time 131.900 Reading energy frame 8 time 149.300 Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (10 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as double precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (3 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as double precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (3 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as double precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (3 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as double precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (10 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as double precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (3 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as double precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (10 ms) 5: [----------] 11 tests from WithParameters/EnergyOutputTest (82 ms total) 5: 5: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms) 5: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (0 ms total) 5: 5: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms) 5: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (0 ms total) 5: 5: [----------] 16 tests from WithParameters/LeapFrogTest 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (2 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (5 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (1 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (3 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (28 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (2 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (2 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (2 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (2 ms) 5: [----------] 16 tests from WithParameters/LeapFrogTest (53 ms total) 5: 5: [----------] 13 tests from WithParameters/SettleTest 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (1 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (1 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (2 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (94 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (70 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (1 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (287 ms) 5: [----------] 13 tests from WithParameters/SettleTest (457 ms total) 5: 5: [----------] Global test environment tear-down 5: [==========] 187 tests from 13 test cases ran. (599 ms total) 5: [ PASSED ] 187 tests. 5/54 Test #5: MdlibUnitTest ....................... Passed 0.66 sec test 6 Start 6: AppliedForcesUnitTest 6: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/applied_forces-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/AppliedForcesUnitTest.xml" 6: Test timeout computed to be: 30 6: [==========] Running 20 tests from 4 test cases. 6: [----------] Global test environment set-up. 6: [----------] 2 tests from DensityFittingTest 6: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows 6: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (1 ms) 6: [ RUN ] DensityFittingTest.SingleAtom 6: [ OK ] DensityFittingTest.SingleAtom (0 ms) 6: [----------] 2 tests from DensityFittingTest (1 ms total) 6: 6: [----------] 8 tests from DensityFittingOptionsTest 6: [ RUN ] DensityFittingOptionsTest.DefaultParameters 6: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) 6: [ RUN ] DensityFittingOptionsTest.OptionSetsActive 6: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms) 6: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive 6: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 6: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive 6: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (0 ms) 6: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup 6: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 6: [ RUN ] DensityFittingOptionsTest.InternalsToKvt 6: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) 6: [ RUN ] DensityFittingOptionsTest.KvtToInternal 6: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms) 6: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent 6: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (1 ms) 6: [----------] 8 tests from DensityFittingOptionsTest (1 ms total) 6: 6: [----------] 7 tests from DensityFittingAmplitudeLookupTest 6: [ RUN ] DensityFittingAmplitudeLookupTest.Unity 6: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.Charge 6: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.Masses 6: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign 6: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct 6: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign 6: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct 6: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) 6: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total) 6: 6: [----------] 3 tests from ElectricFieldTest 6: [ RUN ] ElectricFieldTest.Static 6: [ OK ] ElectricFieldTest.Static (0 ms) 6: [ RUN ] ElectricFieldTest.Oscillating 6: [ OK ] ElectricFieldTest.Oscillating (0 ms) 6: [ RUN ] ElectricFieldTest.Pulsed 6: [ OK ] ElectricFieldTest.Pulsed (0 ms) 6: [----------] 3 tests from ElectricFieldTest (0 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 20 tests from 4 test cases ran. (2 ms total) 6: [ PASSED ] 20 tests. 6/54 Test #6: AppliedForcesUnitTest ............... Passed 0.02 sec test 7 Start 7: CommandLineUnitTests 7: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/commandline-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/CommandLineUnitTests.xml" 7: Test timeout computed to be: 30 7: [==========] Running 59 tests from 7 test cases. 7: [----------] Global test environment set-up. 7: [----------] 3 tests from CommandLineHelpModuleTest 7: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 7: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (1 ms) 7: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 7: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (0 ms) 7: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 7: [ OK ] CommandLineHelpModuleTest.ExportsHelp (1 ms) 7: [----------] 3 tests from CommandLineHelpModuleTest (2 ms total) 7: 7: [----------] 7 tests from CommandLineHelpWriterTest 7: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 7: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (1 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 7: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 7: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 7: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 7: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (1 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 7: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues 7: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms) 7: [----------] 7 tests from CommandLineHelpWriterTest (2 ms total) 7: 7: [----------] 6 tests from CommandLineModuleManagerTest 7: [ RUN ] CommandLineModuleManagerTest.RunsModule 7: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) 7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 7: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 7: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 7: [----------] 6 tests from CommandLineModuleManagerTest (0 ms total) 7: 7: [----------] 13 tests from CommandLineParserTest 7: [ RUN ] CommandLineParserTest.HandlesSingleValues 7: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 7: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 7: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 7: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 7: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 7: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesString 7: [ OK ] CommandLineParserTest.HandlesString (0 ms) 7: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 7: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 7: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 7: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 7: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 7: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 7: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 7: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 7: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 7: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 7: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 7: [----------] 13 tests from CommandLineParserTest (0 ms total) 7: 7: [----------] 6 tests from CommandLineProgramContextTest 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 7: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 7: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 7: [----------] 6 tests from CommandLineProgramContextTest (0 ms total) 7: 7: [----------] 3 tests from OutputNamesTest 7: [ RUN ] OutputNamesTest.CanBeSuffixed 7: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) 7: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend 7: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) 7: [ RUN ] OutputNamesTest.CanHavePartNumberAdded 7: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms) 7: [----------] 3 tests from OutputNamesTest (0 ms total) 7: 7: [----------] 21 tests from ParseCommonArgsTest 7: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 7: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 7: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 7: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 7: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 7: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 7: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (1 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 7: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 7: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 7: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 7: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 7: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 7: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 7: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 7: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 7: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 7: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 7: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 7: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 7: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 7: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 7: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (1 ms) 7: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 7: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 7: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 7: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (3 ms) 7: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 7: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (4 ms) 7: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 7: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 7: [----------] 21 tests from ParseCommonArgsTest (9 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 59 tests from 7 test cases ran. (14 ms total) 7: [ PASSED ] 59 tests. 7/54 Test #7: CommandLineUnitTests ................ Passed 0.03 sec test 8 Start 8: DomDecTests 8: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/domdec-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/DomDecTests.xml" 8: Test timeout computed to be: 30 8: [==========] Running 9 tests from 2 test cases. 8: [----------] Global test environment set-up. 8: [----------] 7 tests from HashedMap 8: [ RUN ] HashedMap.InsertsFinds 8: [ OK ] HashedMap.InsertsFinds (0 ms) 8: [ RUN ] HashedMap.NegativeKeysWork 8: [ OK ] HashedMap.NegativeKeysWork (0 ms) 8: [ RUN ] HashedMap.InsertsErases 8: [ OK ] HashedMap.InsertsErases (0 ms) 8: [ RUN ] HashedMap.InsertsOrAssigns 8: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 8: [ RUN ] HashedMap.Clears 8: [ OK ] HashedMap.Clears (0 ms) 8: [ RUN ] HashedMap.LinkedEntries 8: [ OK ] HashedMap.LinkedEntries (0 ms) 8: [ RUN ] HashedMap.ResizesTable 8: [ OK ] HashedMap.ResizesTable (0 ms) 8: [----------] 7 tests from HashedMap (0 ms total) 8: 8: [----------] 2 tests from LocalAtomSetManager 8: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 8: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 8: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 8: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 8: [----------] 2 tests from LocalAtomSetManager (0 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 9 tests from 2 test cases ran. (0 ms total) 8: [ PASSED ] 9 tests. 8/54 Test #8: DomDecTests ......................... Passed 0.01 sec test 9 Start 9: EwaldUnitTests 9: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/ewald-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/EwaldUnitTests.xml" 9: Test timeout computed to be: 30 9: [==========] Running 257 tests from 10 test cases. 9: [----------] Global test environment set-up. 9: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (1 ms) 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (35 ms) 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 9: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (36 ms total) 9: 9: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (4 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (3 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (3 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (3 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (9 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (4 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (3 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (4 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (4 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (3 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (3 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (3 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (2 ms) 9: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (72 ms total) 9: 9: [----------] 144 tests from SaneInput/PmeGatherTest 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/72 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/72 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/73 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/73 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/74 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/74 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/75 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/75 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/76 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/76 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/77 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/77 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/78 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/78 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/79 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/79 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/80 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/80 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/81 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/81 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/82 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/82 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/83 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/83 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/84 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/84 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/85 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/85 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/86 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/86 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/87 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/87 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/88 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/88 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/89 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/89 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/90 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/90 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/91 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/91 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/92 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/92 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/93 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/93 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/94 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/94 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/95 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/95 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/96 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/96 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/97 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/97 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/98 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/98 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/99 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/99 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/100 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/100 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/101 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/101 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/102 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/102 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/103 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/103 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/104 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/104 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/105 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/105 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/106 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/106 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/107 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/107 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/108 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/108 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/109 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/109 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/110 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/110 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/111 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/111 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/112 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/112 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/113 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/113 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/114 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/114 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/115 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/115 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/116 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/116 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/117 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/117 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/118 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/118 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/119 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/119 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/120 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/120 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/121 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/121 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/122 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/122 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/123 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/123 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/124 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/124 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/125 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/125 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/126 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/126 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/127 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/127 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/128 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/128 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/129 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/129 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/130 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/130 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/131 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/131 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/132 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/132 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/133 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/133 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/134 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/134 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/135 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/135 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/136 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/136 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/137 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/137 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/138 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/138 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/139 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/139 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/140 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/140 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/141 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/141 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/142 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/142 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/143 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/143 (1 ms) 9: [----------] 144 tests from SaneInput/PmeGatherTest (49 ms total) 9: 9: [----------] 16 tests from SaneInput/PmeSolveTest 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (18 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (2 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (2 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (2 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (2 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (2 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (2 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (2 ms) 9: [----------] 16 tests from SaneInput/PmeSolveTest (40 ms total) 9: 9: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (0 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (1 ms) 9: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (7 ms total) 9: 9: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (1 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (2 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (1 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (1 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (2 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (2 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (1 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (1 ms) 9: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (11 ms total) 9: 9: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (2 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (0 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (2 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (0 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (2 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (2 ms) 9: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (18 ms total) 9: 9: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (1 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (4 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (2 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (2 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (2 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (2 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (31 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (2 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (2 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (2 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (3 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (2 ms) 9: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (55 ms total) 9: 9: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (3 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (2 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (51 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (2 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (27 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (2 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (3 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (57 ms) 9: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (152 ms total) 9: 9: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (5 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (5 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (6 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (5 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (6 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (63 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (4 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (32 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (14 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (6 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (7 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (8 ms) 9: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (165 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 257 tests from 10 test cases ran. (708 ms total) 9: [ PASSED ] 257 tests. 9/54 Test #9: EwaldUnitTests ...................... Passed 0.78 sec test 10 Start 10: FFTUnitTests 10: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/fft-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/FFTUnitTests.xml" 10: Test timeout computed to be: 30 10: [==========] Running 14 tests from 4 test cases. 10: [----------] Global test environment set-up. 10: [----------] 2 tests from ManyFFTTest 10: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 10: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (20 ms) 10: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 10: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (26 ms) 10: [----------] 2 tests from ManyFFTTest (47 ms total) 10: 10: [----------] 1 test from FFTTest 10: [ RUN ] FFTTest.Real2DLength18_15Test 10: [ OK ] FFTTest.Real2DLength18_15Test (6 ms) 10: [----------] 1 test from FFTTest (7 ms total) 10: 10: [----------] 1 test from FFFTest3D 10: [ RUN ] FFFTest3D.Real5_6_9 10: [ OK ] FFFTest3D.Real5_6_9 (9 ms) 10: [----------] 1 test from FFFTest3D (10 ms total) 10: 10: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (0 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (1 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (2 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (3 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (3 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (1 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (1 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (1 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (27 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (20 ms) 10: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (60 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 14 tests from 4 test cases ran. (124 ms total) 10: [ PASSED ] 14 tests. 10/54 Test #10: FFTUnitTests ........................ Passed 0.14 sec test 11 Start 11: GpuUtilsUnitTests 11: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/gpu_utils-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/GpuUtilsUnitTests.xml" 11: Test timeout computed to be: 30 11: [==========] Running 62 tests from 20 test cases. 11: [----------] Global test environment set-up. 11: [----------] 2 tests from ClfftInitializer 11: [ RUN ] ClfftInitializer.SingleInitializationWorks 11: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) 11: [ RUN ] ClfftInitializer.TwoInitializationsWork 11: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) 11: [----------] 2 tests from ClfftInitializer (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 11: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 11: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 11: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 11: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = double 11: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 11: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 11: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 11: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 11: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 11: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 11: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 11: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 11: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 11: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 11: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 11: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 11: 11: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 11: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 11: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 11: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 11: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 11: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 11: 11: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = double 11: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 11: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 11: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 11: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 11: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 11: 11: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 11: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 11: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 11: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 11: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 11: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 11: 11: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 11: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 11: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 11: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 11: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/0.Swap 11: [ OK ] HostAllocatorTestNoMem/0.Swap (1 ms) 11: [ RUN ] HostAllocatorTestNoMem/0.Comparison 11: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 11: [----------] 5 tests from HostAllocatorTestNoMem/0 (1 ms total) 11: 11: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = double 11: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 11: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 11: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 11: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/1.Swap 11: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/1.Comparison 11: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 11: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 11: 11: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 11: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 11: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 11: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 11: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/2.Swap 11: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/2.Comparison 11: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 11: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 11: 11: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 11: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 11: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 11: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 11: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/3.Swap 11: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/3.Comparison 11: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 11: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 11: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 11: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 11: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = double 11: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 11: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 11: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 11: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 11: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 11: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 11: 11: [----------] 1 test from HostAllocatorUntypedTest 11: [ RUN ] HostAllocatorUntypedTest.Comparison 11: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 11: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 11: 11: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 11: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/0.Move 11: [ OK ] AllocatorTest/0.Move (0 ms) 11: [----------] 4 tests from AllocatorTest/0 (0 ms total) 11: 11: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 11: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/1.Move 11: [ OK ] AllocatorTest/1.Move (0 ms) 11: [----------] 4 tests from AllocatorTest/1 (0 ms total) 11: 11: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 11: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/2.Move 11: [ OK ] AllocatorTest/2.Move (0 ms) 11: [----------] 4 tests from AllocatorTest/2 (0 ms total) 11: 11: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 11: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (1 ms) 11: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/3.Move 11: [ OK ] AllocatorTest/3.Move (0 ms) 11: [----------] 4 tests from AllocatorTest/3 (1 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 62 tests from 20 test cases ran. (2 ms total) 11: [ PASSED ] 62 tests. 11/54 Test #11: GpuUtilsUnitTests ................... Passed 0.01 sec test 12 Start 12: HardwareUnitTests 12: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/hardware-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/HardwareUnitTests.xml" 12: Test timeout computed to be: 30 12: [==========] Running 4 tests from 1 test case. 12: [----------] Global test environment set-up. 12: [----------] 4 tests from HardwareTopologyTest 12: [ RUN ] HardwareTopologyTest.Execute 12: [ OK ] HardwareTopologyTest.Execute (75 ms) 12: [ RUN ] HardwareTopologyTest.HwlocExecute 12: [ OK ] HardwareTopologyTest.HwlocExecute (41 ms) 12: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 12: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (84 ms) 12: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 12: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (50 ms) 12: [----------] 4 tests from HardwareTopologyTest (250 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 4 tests from 1 test case ran. (250 ms total) 12: [ PASSED ] 4 tests. 12/54 Test #12: HardwareUnitTests ................... Passed 0.26 sec test 13 Start 13: MathUnitTests 13: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/math-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/MathUnitTests.xml" 13: Test timeout computed to be: 30 13: [==========] Running 204 tests from 29 test cases. 13: [----------] Global test environment set-up. 13: [----------] 1 test from EmptyArrayRefWithPaddingTest 13: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 13: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 13: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 13: 13: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 13: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 13: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 13: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 13: 13: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 13: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 13: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 13: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 13: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 13: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 13: 13: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 13: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 13: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 13: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 13: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 13: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 13: 13: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 13: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 13: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 13: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 13: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 13: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 13: 13: [----------] 8 tests from TranslateAndScaleTest 13: [ RUN ] TranslateAndScaleTest.identityTransformation 13: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms) 13: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling 13: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) 13: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation 13: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) 13: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial 13: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (1 ms) 13: [ RUN ] TranslateAndScaleTest.scalingIdentity 13: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms) 13: [ RUN ] TranslateAndScaleTest.scalingNonTrivial 13: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) 13: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero 13: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms) 13: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero 13: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) 13: [----------] 8 tests from TranslateAndScaleTest (1 ms total) 13: 13: [----------] 12 tests from DensitySimilarityTest 13: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect 13: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect 13: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch 13: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms) 13: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch 13: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms) 13: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect 13: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero 13: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (1 ms) 13: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect 13: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect 13: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne 13: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (71 ms) 13: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated 13: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (51 ms) 13: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated 13: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (41 ms) 13: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect 13: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms) 13: [----------] 12 tests from DensitySimilarityTest (164 ms total) 13: 13: [----------] 6 tests from StructureSimilarityTest 13: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 13: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (1 ms) 13: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 13: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 13: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 13: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 13: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 13: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 13: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 13: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 13: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 13: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 13: [----------] 6 tests from StructureSimilarityTest (1 ms total) 13: 13: [----------] 8 tests from ExponentialMovingAverage 13: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero 13: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) 13: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative 13: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) 13: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue 13: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) 13: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue 13: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) 13: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly 13: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) 13: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing 13: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) 13: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect 13: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) 13: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree 13: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) 13: [----------] 8 tests from ExponentialMovingAverage (0 ms total) 13: 13: [----------] 21 tests from FunctionTest 13: [ RUN ] FunctionTest.StaticLog2 13: [ OK ] FunctionTest.StaticLog2 (0 ms) 13: [ RUN ] FunctionTest.Log2I32Bit 13: [ OK ] FunctionTest.Log2I32Bit (0 ms) 13: [ RUN ] FunctionTest.Log2I64Bit 13: [ OK ] FunctionTest.Log2I64Bit (0 ms) 13: [ RUN ] FunctionTest.GreatestCommonDivisor 13: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 13: [ RUN ] FunctionTest.InvsqrtFloat 13: [ OK ] FunctionTest.InvsqrtFloat (1 ms) 13: [ RUN ] FunctionTest.InvsqrtDouble 13: [ OK ] FunctionTest.InvsqrtDouble (0 ms) 13: [ RUN ] FunctionTest.InvsqrtInteger 13: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 13: [ RUN ] FunctionTest.InvcbrtFloat 13: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 13: [ RUN ] FunctionTest.InvcbrtDouble 13: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 13: [ RUN ] FunctionTest.InvcbrtInteger 13: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 13: [ RUN ] FunctionTest.SixthrootFloat 13: [ OK ] FunctionTest.SixthrootFloat (0 ms) 13: [ RUN ] FunctionTest.SixthrootDouble 13: [ OK ] FunctionTest.SixthrootDouble (0 ms) 13: [ RUN ] FunctionTest.SixthrootInteger 13: [ OK ] FunctionTest.SixthrootInteger (1 ms) 13: [ RUN ] FunctionTest.InvsixthrootFloat 13: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 13: [ RUN ] FunctionTest.InvsixthrootDouble 13: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 13: [ RUN ] FunctionTest.InvsixthrootInteger 13: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 13: [ RUN ] FunctionTest.Powers 13: [ OK ] FunctionTest.Powers (0 ms) 13: [ RUN ] FunctionTest.ErfInvFloat 13: [ OK ] FunctionTest.ErfInvFloat (0 ms) 13: [ RUN ] FunctionTest.ErfInvDouble 13: [ OK ] FunctionTest.ErfInvDouble (0 ms) 13: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 13: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 13: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 13: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (1 ms) 13: [----------] 21 tests from FunctionTest (3 ms total) 13: 13: [----------] 4 tests from GaussianOn1DLattice 13: [ RUN ] GaussianOn1DLattice.sumsCloseToOne 13: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) 13: [ RUN ] GaussianOn1DLattice.isCorrect 13: [ OK ] GaussianOn1DLattice.isCorrect (0 ms) 13: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero 13: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) 13: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange 13: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) 13: [----------] 4 tests from GaussianOn1DLattice (0 ms total) 13: 13: [----------] 9 tests from GaussTransformTest 13: [ RUN ] GaussTransformTest.isZeroUponConstruction 13: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) 13: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss 13: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) 13: [ RUN ] GaussTransformTest.isZeroAfterSettingZero 13: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) 13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX 13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) 13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY 13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) 13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ 13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) 13: [ RUN ] GaussTransformTest.complementaryGaussAddToZero 13: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) 13: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues 13: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms) 13: [ RUN ] GaussTransformTest.view 13: [ OK ] GaussTransformTest.view (0 ms) 13: [----------] 9 tests from GaussTransformTest (0 ms total) 13: 13: [----------] 3 tests from DensityFittingForce 13: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity 13: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) 13: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections 13: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) 13: [ RUN ] DensityFittingForce.pullsTowardsDerivative 13: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) 13: [----------] 3 tests from DensityFittingForce (0 ms total) 13: 13: [----------] 2 tests from InvertMatrixTest 13: [ RUN ] InvertMatrixTest.IdentityIsImpotent 13: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 13: [ RUN ] InvertMatrixTest.ComputesInverse 13: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 13: [----------] 2 tests from InvertMatrixTest (0 ms total) 13: 13: [----------] 2 tests from InvertBoxMatrixTest 13: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 13: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 13: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 13: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 13: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 13: 13: [----------] 15 tests from MatrixTest 13: [ RUN ] MatrixTest.canSetFromArray 13: [ OK ] MatrixTest.canSetFromArray (0 ms) 13: [ RUN ] MatrixTest.canSetStaticallyFromList 13: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) 13: [ RUN ] MatrixTest.canConstructAndFill 13: [ OK ] MatrixTest.canConstructAndFill (0 ms) 13: [ RUN ] MatrixTest.canSetValues 13: [ OK ] MatrixTest.canSetValues (0 ms) 13: [ RUN ] MatrixTest.canCopyAssign 13: [ OK ] MatrixTest.canCopyAssign (0 ms) 13: [ RUN ] MatrixTest.canSwap 13: [ OK ] MatrixTest.canSwap (0 ms) 13: [ RUN ] MatrixTest.staticMultiDimArrayExtent 13: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) 13: [ RUN ] MatrixTest.determinantWorks 13: [ OK ] MatrixTest.determinantWorks (0 ms) 13: [ RUN ] MatrixTest.noninvertableDeterminantIsZero 13: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) 13: [ RUN ] MatrixTest.determinantOfDiagonalMatrix 13: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) 13: [ RUN ] MatrixTest.traceWorks 13: [ OK ] MatrixTest.traceWorks (0 ms) 13: [ RUN ] MatrixTest.transposeWorks 13: [ OK ] MatrixTest.transposeWorks (0 ms) 13: [ RUN ] MatrixTest.transposeOfSymmetricMatrix 13: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) 13: [ RUN ] MatrixTest.canCreateFromLegacyMatrix 13: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) 13: [ RUN ] MatrixTest.canFillLegacyMatrix 13: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) 13: [----------] 15 tests from MatrixTest (0 ms total) 13: 13: [----------] 25 tests from MultiDimArrayTest 13: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic 13: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic 13: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canSetValuesInStatic 13: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic 13: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canMoveConstructStatic 13: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic 13: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canMoveAssignStatic 13: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic 13: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canCopyConstructStatic 13: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic 13: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canCopyAssignStatic 13: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic 13: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canSwapStatic 13: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canSwapDynamic 13: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent 13: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) 13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent 13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) 13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent 13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) 13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue 13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) 13: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray 13: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) 13: [ RUN ] MultiDimArrayTest.conversionToView 13: [ OK ] MultiDimArrayTest.conversionToView (0 ms) 13: [ RUN ] MultiDimArrayTest.conversionToConstView 13: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) 13: [ RUN ] MultiDimArrayTest.viewBegin 13: [ OK ] MultiDimArrayTest.viewBegin (0 ms) 13: [ RUN ] MultiDimArrayTest.viewEnd 13: [ OK ] MultiDimArrayTest.viewEnd (0 ms) 13: [ RUN ] MultiDimArrayTest.constViewConstBegin 13: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) 13: [ RUN ] MultiDimArrayTest.constViewConstEnd 13: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) 13: [----------] 25 tests from MultiDimArrayTest (1 ms total) 13: 13: [----------] 4 tests from MultiDimArrayToMdSpanTest 13: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan 13: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) 13: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan 13: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) 13: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan 13: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) 13: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan 13: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) 13: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/0, where TypeParam = std::allocator 13: [ RUN ] PaddedVectorTest/0.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/0.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/0.CanCopyAssign 13: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/0.CanMoveAssign 13: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/0.CanSwap 13: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/0 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/1, where TypeParam = std::allocator 13: [ RUN ] PaddedVectorTest/1.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/1.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/1.CanCopyAssign 13: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/1.CanMoveAssign 13: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/1.CanSwap 13: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/1 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/2, where TypeParam = std::allocator 13: [ RUN ] PaddedVectorTest/2.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/2.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/2.CanCopyAssign 13: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/2.CanMoveAssign 13: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/2.CanSwap 13: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/2 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 13: [ RUN ] PaddedVectorTest/3.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/3.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/3.CanCopyAssign 13: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/3.CanMoveAssign 13: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/3.CanSwap 13: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/3 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 13: [ RUN ] PaddedVectorTest/4.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/4.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/4.CanCopyAssign 13: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/4.CanMoveAssign 13: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/4.CanSwap 13: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/4 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 13: [ RUN ] PaddedVectorTest/5.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/5.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/5.CanCopyAssign 13: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/5.CanMoveAssign 13: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/5.CanSwap 13: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/5 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 13: [ RUN ] PaddedVectorTest/6.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/6.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/6.CanCopyAssign 13: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/6.CanMoveAssign 13: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/6.CanSwap 13: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/6 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 13: [ RUN ] PaddedVectorTest/7.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/7.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/7.CanCopyAssign 13: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/7.CanMoveAssign 13: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/7.CanSwap 13: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/7 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 13: [ RUN ] PaddedVectorTest/8.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/8.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/8.CanCopyAssign 13: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/8.CanMoveAssign 13: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/8.CanSwap 13: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/8 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 13: [ RUN ] PaddedVectorTest/9.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/9.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/9.CanCopyAssign 13: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/9.CanMoveAssign 13: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/9.CanSwap 13: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/9 (0 ms total) 13: 13: [----------] 37 tests from RVecTest 13: [ RUN ] RVecTest.CanBeStoredInVector 13: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 13: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 13: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 13: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 13: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 13: [ RUN ] RVecTest.WorksAsMutable_rvec 13: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 13: [ RUN ] RVecTest.WorksAs_rvec_Array 13: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 13: [ RUN ] RVecTest.CanAddRVecToRvec 13: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 13: [ RUN ] RVecTest.CanAddAssignRVecToRvec 13: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 13: [ RUN ] RVecTest.CanSubtractRVecFromRvec 13: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 13: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 13: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 13: [ RUN ] RVecTest.CanDotProductRVecByRvec 13: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 13: [ RUN ] RVecTest.CanCrossProductRVecByRvec 13: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 13: [ RUN ] RVecTest.CanDivideRVecInplace 13: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 13: [ RUN ] RVecTest.CanScaleRVec 13: [ OK ] RVecTest.CanScaleRVec (0 ms) 13: [ RUN ] RVecTest.CanDivideRVec 13: [ OK ] RVecTest.CanDivideRVec (0 ms) 13: [ RUN ] RVecTest.CanDoUnitvFromRVec 13: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 13: [ RUN ] RVecTest.CanSqLengthOfRVec 13: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 13: [ RUN ] RVecTest.CanLengthOfRVec 13: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 13: [ RUN ] RVecTest.CanCastToRVec 13: [ OK ] RVecTest.CanCastToRVec (0 ms) 13: [ RUN ] RVecTest.CanCastToDVec 13: [ OK ] RVecTest.CanCastToDVec (0 ms) 13: [ RUN ] RVecTest.CanLeftScalarMultiply 13: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 13: [ RUN ] RVecTest.CanRightScalarMultiply 13: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 13: [ RUN ] RVecTest.CanGetUnitvFromRVec 13: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 13: [ RUN ] RVecTest.CanGetSqLengthOfRVec 13: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 13: [ RUN ] RVecTest.CanGetLengthOfRVec 13: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 13: [ RUN ] RVecTest.CanDoCrossProductOfRVec 13: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 13: [ RUN ] RVecTest.CanDoDotProductOfRVec 13: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 13: [ RUN ] RVecTest.CanScaleByVector 13: [ OK ] RVecTest.CanScaleByVector (0 ms) 13: [ RUN ] RVecTest.asIVec 13: [ OK ] RVecTest.asIVec (0 ms) 13: [ RUN ] RVecTest.elementWiseMin 13: [ OK ] RVecTest.elementWiseMin (0 ms) 13: [ RUN ] RVecTest.elementWiseMax 13: [ OK ] RVecTest.elementWiseMax (0 ms) 13: [ RUN ] RVecTest.WorksAs_dvec_Reference 13: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 13: [ RUN ] RVecTest.WorksAs_ivec_Reference 13: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 13: [ RUN ] RVecTest.WorksAs_rvec_Reference 13: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 13: [ RUN ] RVecTest.CopyConstructorWorks 13: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 13: [ RUN ] RVecTest.CopyAssignmentWorks 13: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 13: [ RUN ] RVecTest.MoveConstructorWorks 13: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 13: [ RUN ] RVecTest.MoveAssignmentWorks 13: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 13: [----------] 37 tests from RVecTest (1 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 204 tests from 29 test cases ran. (171 ms total) 13: [ PASSED ] 204 tests. 13/54 Test #13: MathUnitTests ....................... Passed 0.19 sec test 14 Start 14: MdrunUtilityUnitTests 14: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/mdrunutility-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/MdrunUtilityUnitTests.xml" 14: Test timeout computed to be: 30 14: [==========] Running 17 tests from 1 test case. 14: [----------] Global test environment set-up. 14: [----------] 17 tests from ThreadAffinityTest 14: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 14: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 14: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 14: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (1 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 14: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 14: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 14: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 14: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) 14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 14: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (1 ms) 14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 14: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (0 ms) 14: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 14: NOTE: Affinity setting failed. 14: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) 14: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 14: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (1 ms) 14: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 14: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (0 ms) 14: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 14: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (0 ms) 14: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 14: NOTE: Affinity setting for 1/2 threads failed. 14: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (1 ms) 14: [----------] 17 tests from ThreadAffinityTest (4 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 17 tests from 1 test case ran. (4 ms total) 14: [ PASSED ] 17 tests. 14/54 Test #14: MdrunUtilityUnitTests ............... Passed 0.02 sec test 15 Start 15: MdrunUtilityMpiUnitTests 15: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 15: Test timeout computed to be: 30 15: [==========] Running 13 tests from 2 test cases. 15: [----------] Global test environment set-up. 15: [----------] 6 tests from ThreadAffinityMultiRankTest 15: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 15: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (2 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 15: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (2 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 15: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (1 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 15: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (0 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 15: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (0 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 15: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (0 ms) 15: [----------] 6 tests from ThreadAffinityMultiRankTest (6 ms total) 15: 15: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (50 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (1 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (1 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (1 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (1 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (1 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (16 ms) 15: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (72 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 13 tests from 2 test cases ran. (78 ms total) 15: [ PASSED ] 13 tests. 15/54 Test #15: MdrunUtilityMpiUnitTests ............ Passed 0.09 sec test 16 Start 16: MDSpanTests 16: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/mdspan-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/MDSpanTests.xml" 16: Test timeout computed to be: 30 16: [==========] Running 32 tests from 7 test cases. 16: [----------] Global test environment set-up. 16: [----------] 4 tests from BasicAccessorPolicy 16: [ RUN ] BasicAccessorPolicy.Decay 16: [ OK ] BasicAccessorPolicy.Decay (0 ms) 16: [ RUN ] BasicAccessorPolicy.Access 16: [ OK ] BasicAccessorPolicy.Access (0 ms) 16: [ RUN ] BasicAccessorPolicy.Offset 16: [ OK ] BasicAccessorPolicy.Offset (0 ms) 16: [ RUN ] BasicAccessorPolicy.CopyAccessor 16: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) 16: [----------] 4 tests from BasicAccessorPolicy (0 ms total) 16: 16: [----------] 4 tests from ExtentsTest 16: [ RUN ] ExtentsTest.Construction 16: [ OK ] ExtentsTest.Construction (0 ms) 16: [ RUN ] ExtentsTest.PurelyStatic 16: [ OK ] ExtentsTest.PurelyStatic (0 ms) 16: [ RUN ] ExtentsTest.RankNought 16: [ OK ] ExtentsTest.RankNought (0 ms) 16: [ RUN ] ExtentsTest.Assignment 16: [ OK ] ExtentsTest.Assignment (0 ms) 16: [----------] 4 tests from ExtentsTest (0 ms total) 16: 16: [----------] 8 tests from MdSpanExtension 16: [ RUN ] MdSpanExtension.SlicingAllStatic 16: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) 16: [ RUN ] MdSpanExtension.SlicingDynamic 16: [ OK ] MdSpanExtension.SlicingDynamic (0 ms) 16: [ RUN ] MdSpanExtension.SlicingAllStatic3D 16: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) 16: [ RUN ] MdSpanExtension.SlicingEqualsView3D 16: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) 16: [ RUN ] MdSpanExtension.additionWorks 16: [ OK ] MdSpanExtension.additionWorks (0 ms) 16: [ RUN ] MdSpanExtension.subtractionWorks 16: [ OK ] MdSpanExtension.subtractionWorks (0 ms) 16: [ RUN ] MdSpanExtension.multiplicationWorks 16: [ OK ] MdSpanExtension.multiplicationWorks (0 ms) 16: [ RUN ] MdSpanExtension.divisionWorks 16: [ OK ] MdSpanExtension.divisionWorks (0 ms) 16: [----------] 8 tests from MdSpanExtension (0 ms total) 16: 16: [----------] 3 tests from LayoutTests 16: [ RUN ] LayoutTests.LayoutRightConstruction 16: [ OK ] LayoutTests.LayoutRightConstruction (0 ms) 16: [ RUN ] LayoutTests.LayoutRightProperties 16: [ OK ] LayoutTests.LayoutRightProperties (0 ms) 16: [ RUN ] LayoutTests.LayoutRightOperator 16: [ OK ] LayoutTests.LayoutRightOperator (0 ms) 16: [----------] 3 tests from LayoutTests (0 ms total) 16: 16: [----------] 1 test from MdSpanTest 16: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly 16: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) 16: [----------] 1 test from MdSpanTest (0 ms total) 16: 16: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 16: [ RUN ] MdSpanTest/0.Rank 16: [ OK ] MdSpanTest/0.Rank (0 ms) 16: [ RUN ] MdSpanTest/0.DynamicRank 16: [ OK ] MdSpanTest/0.DynamicRank (0 ms) 16: [ RUN ] MdSpanTest/0.Extents 16: [ OK ] MdSpanTest/0.Extents (0 ms) 16: [ RUN ] MdSpanTest/0.Strides 16: [ OK ] MdSpanTest/0.Strides (0 ms) 16: [ RUN ] MdSpanTest/0.Properties 16: [ OK ] MdSpanTest/0.Properties (0 ms) 16: [ RUN ] MdSpanTest/0.Operator 16: [ OK ] MdSpanTest/0.Operator (0 ms) 16: [----------] 6 tests from MdSpanTest/0 (0 ms total) 16: 16: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 16: [ RUN ] MdSpanTest/1.Rank 16: [ OK ] MdSpanTest/1.Rank (0 ms) 16: [ RUN ] MdSpanTest/1.DynamicRank 16: [ OK ] MdSpanTest/1.DynamicRank (0 ms) 16: [ RUN ] MdSpanTest/1.Extents 16: [ OK ] MdSpanTest/1.Extents (0 ms) 16: [ RUN ] MdSpanTest/1.Strides 16: [ OK ] MdSpanTest/1.Strides (0 ms) 16: [ RUN ] MdSpanTest/1.Properties 16: [ OK ] MdSpanTest/1.Properties (0 ms) 16: [ RUN ] MdSpanTest/1.Operator 16: [ OK ] MdSpanTest/1.Operator (0 ms) 16: [----------] 6 tests from MdSpanTest/1 (0 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 32 tests from 7 test cases ran. (0 ms total) 16: [ PASSED ] 32 tests. 16/54 Test #16: MDSpanTests ......................... Passed 0.08 sec test 17 Start 17: OnlineHelpUnitTests 17: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/onlinehelp-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/OnlineHelpUnitTests.xml" 17: Test timeout computed to be: 30 17: [==========] Running 22 tests from 4 test cases. 17: [----------] Global test environment set-up. 17: [----------] 6 tests from TextTableFormatterTest 17: [ RUN ] TextTableFormatterTest.HandlesBasicCase 17: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms) 17: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 17: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) 17: [ RUN ] TextTableFormatterTest.HandlesIndentation 17: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) 17: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 17: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) 17: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 17: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (1 ms) 17: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 17: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) 17: [----------] 6 tests from TextTableFormatterTest (1 ms total) 17: 17: [----------] 3 tests from HelpManagerTest 17: [ RUN ] HelpManagerTest.HandlesRootTopic 17: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 17: [ RUN ] HelpManagerTest.HandlesSubTopics 17: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 17: [ RUN ] HelpManagerTest.HandlesInvalidTopics 17: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 17: [----------] 3 tests from HelpManagerTest (0 ms total) 17: 17: [----------] 2 tests from HelpTopicFormattingTest 17: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 17: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms) 17: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 17: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) 17: [----------] 2 tests from HelpTopicFormattingTest (0 ms total) 17: 17: [----------] 11 tests from HelpWriterContextTest 17: [ RUN ] HelpWriterContextTest.FormatsParagraphs 17: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 17: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 17: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 17: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsLiteralText 17: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 17: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 17: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsBulletList 17: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 17: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 17: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsGridTable 17: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsTitles 17: [ OK ] HelpWriterContextTest.FormatsTitles (1 ms) 17: [----------] 11 tests from HelpWriterContextTest (2 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 22 tests from 4 test cases ran. (3 ms total) 17: [ PASSED ] 22 tests. 17/54 Test #17: OnlineHelpUnitTests ................. Passed 0.01 sec test 18 Start 18: OptionsUnitTests 18: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/options-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/OptionsUnitTests.xml" 18: Test timeout computed to be: 30 18: [==========] Running 110 tests from 18 test cases. 18: [----------] Global test environment set-up. 18: [----------] 5 tests from AbstractOptionStorageTest 18: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 18: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 18: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 18: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) 18: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 18: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (1 ms) 18: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 18: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 18: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 18: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 18: [----------] 5 tests from AbstractOptionStorageTest (1 ms total) 18: 18: [----------] 8 tests from FileNameOptionTest 18: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 18: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 18: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 18: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 18: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 18: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 18: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 18: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 18: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 18: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 18: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 18: [----------] 8 tests from FileNameOptionTest (0 ms total) 18: 18: [----------] 15 tests from FileNameOptionManagerTest 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 18: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (1 ms) 18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 18: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 18: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 18: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 18: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 18: [----------] 15 tests from FileNameOptionManagerTest (1 ms total) 18: 18: [----------] 1 test from OptionsTest 18: [ RUN ] OptionsTest.FailsOnNonsafeStorage 18: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 18: [----------] 1 test from OptionsTest (0 ms total) 18: 18: [----------] 9 tests from OptionsAssignerTest 18: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 18: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 18: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 18: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 18: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesMissingValue 18: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesExtraValue 18: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesGroups 18: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesSections 18: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 18: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 18: [----------] 9 tests from OptionsAssignerTest (0 ms total) 18: 18: [----------] 4 tests from OptionsAssignerBooleanTest 18: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 18: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 18: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 18: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 18: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 18: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 18: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 18: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 18: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 18: 18: [----------] 13 tests from OptionsAssignerIntegerTest 18: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 18: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 18: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 18: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 18: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 18: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 18: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 18: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 18: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 18: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 18: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 18: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total) 18: 18: [----------] 5 tests from OptionsAssignerDoubleTest 18: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 18: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 18: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 18: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 18: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 18: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 18: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 18: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 18: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 18: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 18: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 18: 18: [----------] 9 tests from OptionsAssignerStringTest 18: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 18: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 18: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 18: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 18: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 18: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 18: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 18: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 18: 18: [----------] 6 tests from OptionsAssignerEnumTest 18: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 18: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 18: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 18: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 18: [----------] 6 tests from OptionsAssignerEnumTest (1 ms total) 18: 18: [----------] 8 tests from RepeatingOptionSectionTest 18: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 18: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 18: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 18: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 18: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 18: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 18: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 18: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 18: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 18: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 18: 18: [----------] 1 test from TimeUnitManagerTest 18: [ RUN ] TimeUnitManagerTest.BasicOperations 18: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 18: [----------] 1 test from TimeUnitManagerTest (0 ms total) 18: 18: [----------] 4 tests from TimeUnitBehaviorTest 18: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 18: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 18: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 18: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 18: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 18: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 18: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 18: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 18: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 18: 18: [----------] 2 tests from TreeValueSupportAssignTest 18: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 18: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 18: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 18: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 18: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) 18: 18: [----------] 1 test from TreeValueSupportAssignErrorTest 18: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 18: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 18: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 18: 18: [----------] 5 tests from TreeValueSupportCheckTest 18: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 18: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 18: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 18: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 18: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 18: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 18: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 18: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 18: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 18: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 18: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 18: 18: [----------] 6 tests from TreeValueSupportAdjustTest 18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (1 ms) 18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) 18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms) 18: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 18: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 18: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 18: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) 18: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 18: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 18: [----------] 6 tests from TreeValueSupportAdjustTest (1 ms total) 18: 18: [----------] 8 tests from TreeValueSupportTest 18: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 18: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 18: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsInt64Option 18: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsStringOption 18: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsFloatOption 18: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 18: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsEnumIntOption 18: [ OK ] TreeValueSupportTest.SupportsEnumIntOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsEnumOption 18: [ OK ] TreeValueSupportTest.SupportsEnumOption (1 ms) 18: [----------] 8 tests from TreeValueSupportTest (2 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 110 tests from 18 test cases ran. (7 ms total) 18: [ PASSED ] 110 tests. 18/54 Test #18: OptionsUnitTests .................... Passed 0.03 sec test 19 Start 19: PbcutilUnitTest 19: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/pbcutil-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/PbcutilUnitTest.xml" 19: Test timeout computed to be: 30 19: [==========] Running 3 tests from 2 test cases. 19: [----------] Global test environment set-up. 19: [----------] 1 test from PbcTest 19: [ RUN ] PbcTest.CalcShiftsWorks 19: [ OK ] PbcTest.CalcShiftsWorks (0 ms) 19: [----------] 1 test from PbcTest (0 ms total) 19: 19: [----------] 2 tests from PbcEnumsTest 19: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect 19: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms) 19: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect 19: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) 19: [----------] 2 tests from PbcEnumsTest (0 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 3 tests from 2 test cases ran. (0 ms total) 19: [ PASSED ] 3 tests. 19/54 Test #19: PbcutilUnitTest ..................... Passed 0.01 sec test 20 Start 20: RandomUnitTests 20: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/random-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/RandomUnitTests.xml" 20: Test timeout computed to be: 30 20: [==========] Running 44 tests from 10 test cases. 20: [----------] Global test environment set-up. 20: [----------] 4 tests from ExponentialDistributionTest 20: [ RUN ] ExponentialDistributionTest.Output 20: [ OK ] ExponentialDistributionTest.Output (0 ms) 20: [ RUN ] ExponentialDistributionTest.Logical 20: [ OK ] ExponentialDistributionTest.Logical (0 ms) 20: [ RUN ] ExponentialDistributionTest.Reset 20: [ OK ] ExponentialDistributionTest.Reset (0 ms) 20: [ RUN ] ExponentialDistributionTest.AltParam 20: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 20: [----------] 4 tests from ExponentialDistributionTest (0 ms total) 20: 20: [----------] 4 tests from GammaDistributionTest 20: [ RUN ] GammaDistributionTest.Output 20: [ OK ] GammaDistributionTest.Output (0 ms) 20: [ RUN ] GammaDistributionTest.Logical 20: [ OK ] GammaDistributionTest.Logical (0 ms) 20: [ RUN ] GammaDistributionTest.Reset 20: [ OK ] GammaDistributionTest.Reset (0 ms) 20: [ RUN ] GammaDistributionTest.AltParam 20: [ OK ] GammaDistributionTest.AltParam (0 ms) 20: [----------] 4 tests from GammaDistributionTest (0 ms total) 20: 20: [----------] 4 tests from NormalDistributionTest 20: [ RUN ] NormalDistributionTest.Output 20: [ OK ] NormalDistributionTest.Output (0 ms) 20: [ RUN ] NormalDistributionTest.Logical 20: [ OK ] NormalDistributionTest.Logical (0 ms) 20: [ RUN ] NormalDistributionTest.Reset 20: [ OK ] NormalDistributionTest.Reset (0 ms) 20: [ RUN ] NormalDistributionTest.AltParam 20: [ OK ] NormalDistributionTest.AltParam (0 ms) 20: [----------] 4 tests from NormalDistributionTest (0 ms total) 20: 20: [----------] 1 test from SeedTest 20: [ RUN ] SeedTest.makeRandomSeed 20: [ OK ] SeedTest.makeRandomSeed (1 ms) 20: [----------] 1 test from SeedTest (1 ms total) 20: 20: [----------] 6 tests from TabulatedNormalDistributionTest 20: [ RUN ] TabulatedNormalDistributionTest.Output14 20: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) 20: [ RUN ] TabulatedNormalDistributionTest.Output16 20: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) 20: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 20: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) 20: [ RUN ] TabulatedNormalDistributionTest.Logical 20: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 20: [ RUN ] TabulatedNormalDistributionTest.Reset 20: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 20: [ RUN ] TabulatedNormalDistributionTest.AltParam 20: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 20: [----------] 6 tests from TabulatedNormalDistributionTest (0 ms total) 20: 20: [----------] 1 test from TabulatedNormalDistributionTableTest 20: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 20: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (1 ms) 20: [----------] 1 test from TabulatedNormalDistributionTableTest (1 ms total) 20: 20: [----------] 6 tests from ThreeFry2x64Test 20: [ RUN ] ThreeFry2x64Test.Logical 20: [ OK ] ThreeFry2x64Test.Logical (0 ms) 20: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 20: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) 20: [ RUN ] ThreeFry2x64Test.Reseed 20: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 20: [ RUN ] ThreeFry2x64Test.Discard 20: [ OK ] ThreeFry2x64Test.Discard (0 ms) 20: [ RUN ] ThreeFry2x64Test.InvalidCounter 20: [ OK ] ThreeFry2x64Test.InvalidCounter (1 ms) 20: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 20: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 20: [----------] 6 tests from ThreeFry2x64Test (1 ms total) 20: 20: [----------] 4 tests from UniformIntDistributionTest 20: [ RUN ] UniformIntDistributionTest.Output 20: [ OK ] UniformIntDistributionTest.Output (0 ms) 20: [ RUN ] UniformIntDistributionTest.Logical 20: [ OK ] UniformIntDistributionTest.Logical (0 ms) 20: [ RUN ] UniformIntDistributionTest.Reset 20: [ OK ] UniformIntDistributionTest.Reset (0 ms) 20: [ RUN ] UniformIntDistributionTest.AltParam 20: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 20: [----------] 4 tests from UniformIntDistributionTest (0 ms total) 20: 20: [----------] 5 tests from UniformRealDistributionTest 20: [ RUN ] UniformRealDistributionTest.GenerateCanonical 20: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 20: [ RUN ] UniformRealDistributionTest.Output 20: [ OK ] UniformRealDistributionTest.Output (0 ms) 20: [ RUN ] UniformRealDistributionTest.Logical 20: [ OK ] UniformRealDistributionTest.Logical (0 ms) 20: [ RUN ] UniformRealDistributionTest.Reset 20: [ OK ] UniformRealDistributionTest.Reset (0 ms) 20: [ RUN ] UniformRealDistributionTest.AltParam 20: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 20: [----------] 5 tests from UniformRealDistributionTest (0 ms total) 20: 20: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 20: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (1 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 44 tests from 10 test cases ran. (4 ms total) 20: [ PASSED ] 44 tests. 20/54 Test #20: RandomUnitTests ..................... Passed 0.06 sec test 21 Start 21: RestraintTests 21: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/restraintpotential-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/RestraintTests.xml" 21: Test timeout computed to be: 30 21: [==========] Running 1 test from 1 test case. 21: [----------] Global test environment set-up. 21: [----------] 1 test from RestraintManager 21: [ RUN ] RestraintManager.restraintList 21: [ OK ] RestraintManager.restraintList (0 ms) 21: [----------] 1 test from RestraintManager (0 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 1 test from 1 test case ran. (0 ms total) 21: [ PASSED ] 1 test. 21/54 Test #21: RestraintTests ...................... Passed 0.01 sec test 22 Start 22: TableUnitTests 22: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/table-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/TableUnitTests.xml" 22: Test timeout computed to be: 30 22: [==========] Running 20 tests from 2 test cases. 22: [----------] Global test environment set-up. 22: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 22: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 22: [ OK ] SplineTableTest/0.HandlesIncorrectInput (1 ms) 22: [ RUN ] SplineTableTest/0.Sinc 22: [ OK ] SplineTableTest/0.Sinc (1 ms) 22: [ RUN ] SplineTableTest/0.LJ12 22: [ OK ] SplineTableTest/0.LJ12 (14 ms) 22: [ RUN ] SplineTableTest/0.PmeCorrection 22: [ OK ] SplineTableTest/0.PmeCorrection (1 ms) 22: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 22: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (0 ms) 22: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 22: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (1 ms) 22: [ RUN ] SplineTableTest/0.TwoFunctions 22: [ OK ] SplineTableTest/0.TwoFunctions (56 ms) 22: [ RUN ] SplineTableTest/0.ThreeFunctions 22: [ OK ] SplineTableTest/0.ThreeFunctions (36 ms) 22: [ RUN ] SplineTableTest/0.Simd 22: [ OK ] SplineTableTest/0.Simd (7 ms) 22: [ RUN ] SplineTableTest/0.SimdTwoFunctions 22: [ OK ] SplineTableTest/0.SimdTwoFunctions (52 ms) 22: [----------] 10 tests from SplineTableTest/0 (169 ms total) 22: 22: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 22: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 22: [ OK ] SplineTableTest/1.HandlesIncorrectInput (2 ms) 22: [ RUN ] SplineTableTest/1.Sinc 22: [ OK ] SplineTableTest/1.Sinc (1 ms) 22: [ RUN ] SplineTableTest/1.LJ12 22: [ OK ] SplineTableTest/1.LJ12 (43 ms) 22: [ RUN ] SplineTableTest/1.PmeCorrection 22: [ OK ] SplineTableTest/1.PmeCorrection (2 ms) 22: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 22: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms) 22: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 22: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (30 ms) 22: [ RUN ] SplineTableTest/1.TwoFunctions 22: [ OK ] SplineTableTest/1.TwoFunctions (113 ms) 22: [ RUN ] SplineTableTest/1.ThreeFunctions 22: [ OK ] SplineTableTest/1.ThreeFunctions (108 ms) 22: [ RUN ] SplineTableTest/1.Simd 22: [ OK ] SplineTableTest/1.Simd (18 ms) 22: [ RUN ] SplineTableTest/1.SimdTwoFunctions 22: [ OK ] SplineTableTest/1.SimdTwoFunctions (96 ms) 22: [----------] 10 tests from SplineTableTest/1 (413 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 20 tests from 2 test cases ran. (582 ms total) 22: [ PASSED ] 20 tests. 22/54 Test #22: TableUnitTests ...................... Passed 0.60 sec test 23 Start 23: TaskAssignmentUnitTests 23: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/taskassignment-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/TaskAssignmentUnitTests.xml" 23: Test timeout computed to be: 30 23: [==========] Running 3 tests from 2 test cases. 23: [----------] Global test environment set-up. 23: [----------] 2 tests from UserTaskAssignmentStringHandlingTest 23: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork 23: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms) 23: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid 23: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) 23: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total) 23: 23: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest 23: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow 23: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (1 ms) 23: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (1 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 3 tests from 2 test cases ran. (1 ms total) 23: [ PASSED ] 3 tests. 23/54 Test #23: TaskAssignmentUnitTests ............. Passed 0.01 sec test 24 Start 24: TopologyTest 24: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/topology-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/TopologyTest.xml" 24: Test timeout computed to be: 30 24: [==========] Running 11 tests from 3 test cases. 24: [----------] Global test environment set-up. 24: [----------] 3 tests from ExclusionBlockTest 24: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks 24: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) 24: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka 24: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) 24: [ RUN ] ExclusionBlockTest.MergeExclusions 24: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) 24: [----------] 3 tests from ExclusionBlockTest (0 ms total) 24: 24: [----------] 2 tests from MtopTest 24: [ RUN ] MtopTest.RangeBasedLoop 24: [ OK ] MtopTest.RangeBasedLoop (0 ms) 24: [ RUN ] MtopTest.Operators 24: [ OK ] MtopTest.Operators (0 ms) 24: [----------] 2 tests from MtopTest (0 ms total) 24: 24: [----------] 6 tests from SymtabTest 24: [ RUN ] SymtabTest.EmptyOnOpen 24: [ OK ] SymtabTest.EmptyOnOpen (0 ms) 24: [ RUN ] SymtabTest.AddSingleEntry 24: [ OK ] SymtabTest.AddSingleEntry (0 ms) 24: [ RUN ] SymtabTest.AddTwoDistinctEntries 24: [ OK ] SymtabTest.AddTwoDistinctEntries (0 ms) 24: [ RUN ] SymtabTest.TryToAddDuplicates 24: [ OK ] SymtabTest.TryToAddDuplicates (0 ms) 24: [ RUN ] SymtabTest.AddLargeNumberOfEntries 24: [ OK ] SymtabTest.AddLargeNumberOfEntries (0 ms) 24: [ RUN ] SymtabTest.NoDuplicatesInLargeTable 24: [ OK ] SymtabTest.NoDuplicatesInLargeTable (0 ms) 24: [----------] 6 tests from SymtabTest (0 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 11 tests from 3 test cases ran. (0 ms total) 24: [ PASSED ] 11 tests. 24/54 Test #24: TopologyTest ........................ Passed 0.01 sec test 25 Start 25: PullTest 25: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/pull-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/PullTest.xml" 25: Test timeout computed to be: 30 25: [==========] Running 5 tests from 1 test case. 25: [----------] Global test environment set-up. 25: [----------] 5 tests from PullTest 25: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 25: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 25: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 25: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 25: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 25: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 25: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 25: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 25: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 25: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 25: [----------] 5 tests from PullTest (0 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 5 tests from 1 test case ran. (0 ms total) 25: [ PASSED ] 5 tests. 25/54 Test #25: PullTest ............................ Passed 0.04 sec test 26 Start 26: AwhTest 26: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/awh-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/AwhTest.xml" 26: Test timeout computed to be: 30 26: [==========] Running 12 tests from 4 test cases. 26: [----------] Global test environment set-up. 26: [----------] 1 test from BiasTest 26: [ RUN ] BiasTest.DetectsCovering 26: [ OK ] BiasTest.DetectsCovering (1 ms) 26: [----------] 1 test from BiasTest (1 ms total) 26: 26: [----------] 1 test from gridTest 26: [ RUN ] gridTest.neighborhood 26: [ OK ] gridTest.neighborhood (1 ms) 26: [----------] 1 test from gridTest (1 ms total) 26: 26: [----------] 8 tests from WithParameters/BiasTest 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (1 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (0 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (0 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (1 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (0 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (1 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (0 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (1 ms) 26: [----------] 8 tests from WithParameters/BiasTest (5 ms total) 26: 26: [----------] 2 tests from WithParameters/BiasStateTest 26: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 26: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (7 ms) 26: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 26: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms) 26: [----------] 2 tests from WithParameters/BiasStateTest (7 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 12 tests from 4 test cases ran. (14 ms total) 26: [ PASSED ] 12 tests. 26/54 Test #26: AwhTest ............................. Passed 0.03 sec test 27 Start 27: SimdUnitTests 27: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/simd-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/SimdUnitTests.xml" 27: Test timeout computed to be: 30 27: [==========] Running 247 tests from 19 test cases. 27: [----------] Global test environment set-up. 27: [----------] 6 tests from SimdBootstrapTest 27: [ RUN ] SimdBootstrapTest.loadStore 27: [ OK ] SimdBootstrapTest.loadStore (0 ms) 27: [ RUN ] SimdBootstrapTest.loadU 27: [ OK ] SimdBootstrapTest.loadU (0 ms) 27: [ RUN ] SimdBootstrapTest.storeU 27: [ OK ] SimdBootstrapTest.storeU (0 ms) 27: [ RUN ] SimdBootstrapTest.loadStoreI 27: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) 27: [ RUN ] SimdBootstrapTest.loadUI 27: [ OK ] SimdBootstrapTest.loadUI (0 ms) 27: [ RUN ] SimdBootstrapTest.storeUI 27: [ OK ] SimdBootstrapTest.storeUI (0 ms) 27: [----------] 6 tests from SimdBootstrapTest (0 ms total) 27: 27: [----------] 1 test from SimdTest 27: [ RUN ] SimdTest.GmxAligned 27: [ OK ] SimdTest.GmxAligned (0 ms) 27: [----------] 1 test from SimdTest (0 ms total) 27: 27: [----------] 42 tests from SimdFloatingpointTest 27: [ RUN ] SimdFloatingpointTest.setZero 27: [ OK ] SimdFloatingpointTest.setZero (0 ms) 27: [ RUN ] SimdFloatingpointTest.set 27: [ OK ] SimdFloatingpointTest.set (0 ms) 27: [ RUN ] SimdFloatingpointTest.add 27: [ OK ] SimdFloatingpointTest.add (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskAdd 27: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) 27: [ RUN ] SimdFloatingpointTest.sub 27: [ OK ] SimdFloatingpointTest.sub (0 ms) 27: [ RUN ] SimdFloatingpointTest.mul 27: [ OK ] SimdFloatingpointTest.mul (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskzMul 27: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) 27: [ RUN ] SimdFloatingpointTest.fma 27: [ OK ] SimdFloatingpointTest.fma (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskzFma 27: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) 27: [ RUN ] SimdFloatingpointTest.fms 27: [ OK ] SimdFloatingpointTest.fms (0 ms) 27: [ RUN ] SimdFloatingpointTest.fnma 27: [ OK ] SimdFloatingpointTest.fnma (0 ms) 27: [ RUN ] SimdFloatingpointTest.fnms 27: [ OK ] SimdFloatingpointTest.fnms (0 ms) 27: [ RUN ] SimdFloatingpointTest.abs 27: [ OK ] SimdFloatingpointTest.abs (0 ms) 27: [ RUN ] SimdFloatingpointTest.neg 27: [ OK ] SimdFloatingpointTest.neg (0 ms) 27: [ RUN ] SimdFloatingpointTest.and 27: [ OK ] SimdFloatingpointTest.and (0 ms) 27: [ RUN ] SimdFloatingpointTest.or 27: [ OK ] SimdFloatingpointTest.or (0 ms) 27: [ RUN ] SimdFloatingpointTest.xor 27: [ OK ] SimdFloatingpointTest.xor (0 ms) 27: [ RUN ] SimdFloatingpointTest.andNot 27: [ OK ] SimdFloatingpointTest.andNot (0 ms) 27: [ RUN ] SimdFloatingpointTest.max 27: [ OK ] SimdFloatingpointTest.max (0 ms) 27: [ RUN ] SimdFloatingpointTest.min 27: [ OK ] SimdFloatingpointTest.min (0 ms) 27: [ RUN ] SimdFloatingpointTest.round 27: [ OK ] SimdFloatingpointTest.round (0 ms) 27: [ RUN ] SimdFloatingpointTest.roundMode 27: [ OK ] SimdFloatingpointTest.roundMode (0 ms) 27: [ RUN ] SimdFloatingpointTest.trunc 27: [ OK ] SimdFloatingpointTest.trunc (0 ms) 27: [ RUN ] SimdFloatingpointTest.frexp 27: [ OK ] SimdFloatingpointTest.frexp (0 ms) 27: [ RUN ] SimdFloatingpointTest.ldexp 27: [ OK ] SimdFloatingpointTest.ldexp (0 ms) 27: [ RUN ] SimdFloatingpointTest.rsqrt 27: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskzRsqrt 27: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) 27: [ RUN ] SimdFloatingpointTest.rcp 27: [ OK ] SimdFloatingpointTest.rcp (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskzRcp 27: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) 27: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask 27: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) 27: [ RUN ] SimdFloatingpointTest.selectByNotMask 27: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) 27: [ RUN ] SimdFloatingpointTest.cmpNe 27: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) 27: [ RUN ] SimdFloatingpointTest.cmpLe 27: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) 27: [ RUN ] SimdFloatingpointTest.cmpLt 27: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) 27: [ RUN ] SimdFloatingpointTest.testBits 27: [ OK ] SimdFloatingpointTest.testBits (0 ms) 27: [ RUN ] SimdFloatingpointTest.andB 27: [ OK ] SimdFloatingpointTest.andB (0 ms) 27: [ RUN ] SimdFloatingpointTest.orB 27: [ OK ] SimdFloatingpointTest.orB (0 ms) 27: [ RUN ] SimdFloatingpointTest.anyTrueB 27: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) 27: [ RUN ] SimdFloatingpointTest.blend 27: [ OK ] SimdFloatingpointTest.blend (0 ms) 27: [ RUN ] SimdFloatingpointTest.reduce 27: [ OK ] SimdFloatingpointTest.reduce (0 ms) 27: [ RUN ] SimdFloatingpointTest.cvtFloat2Double 27: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) 27: [ RUN ] SimdFloatingpointTest.cvtDouble2Float 27: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) 27: [----------] 42 tests from SimdFloatingpointTest (0 ms total) 27: 27: [----------] 13 tests from SimdFloatingpointUtilTest 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets 27: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum 27: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) 27: [----------] 13 tests from SimdFloatingpointUtilTest (0 ms total) 27: 27: [----------] 3 tests from SimdVectorOperationsTest 27: [ RUN ] SimdVectorOperationsTest.iprod 27: [ OK ] SimdVectorOperationsTest.iprod (0 ms) 27: [ RUN ] SimdVectorOperationsTest.norm2 27: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) 27: [ RUN ] SimdVectorOperationsTest.cprod 27: [ OK ] SimdVectorOperationsTest.cprod (0 ms) 27: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) 27: 27: [----------] 56 tests from SimdMathTest 27: [ RUN ] SimdMathTest.generateTestPointsDouble 27: [ OK ] SimdMathTest.generateTestPointsDouble (1 ms) 27: [ RUN ] SimdMathTest.copysign 27: [ OK ] SimdMathTest.copysign (0 ms) 27: [ RUN ] SimdMathTest.invsqrt 27: [ OK ] SimdMathTest.invsqrt (1 ms) 27: [ RUN ] SimdMathTest.maskzInvsqrt 27: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) 27: [ RUN ] SimdMathTest.invsqrtPair 27: [ OK ] SimdMathTest.invsqrtPair (1 ms) 27: [ RUN ] SimdMathTest.sqrt 27: [ OK ] SimdMathTest.sqrt (2 ms) 27: [ RUN ] SimdMathTest.sqrtUnsafe 27: [ OK ] SimdMathTest.sqrtUnsafe (0 ms) 27: [ RUN ] SimdMathTest.inv 27: [ OK ] SimdMathTest.inv (2 ms) 27: [ RUN ] SimdMathTest.maskzInv 27: [ OK ] SimdMathTest.maskzInv (0 ms) 27: [ RUN ] SimdMathTest.cbrt 27: [ OK ] SimdMathTest.cbrt (2 ms) 27: [ RUN ] SimdMathTest.invcbrt 27: [ OK ] SimdMathTest.invcbrt (2 ms) 27: [ RUN ] SimdMathTest.log2 27: [ OK ] SimdMathTest.log2 (1 ms) 27: [ RUN ] SimdMathTest.log 27: [ OK ] SimdMathTest.log (1 ms) 27: [ RUN ] SimdMathTest.exp2 27: [ OK ] SimdMathTest.exp2 (4 ms) 27: [ RUN ] SimdMathTest.exp2Unsafe 27: [ OK ] SimdMathTest.exp2Unsafe (0 ms) 27: [ RUN ] SimdMathTest.exp 27: [ OK ] SimdMathTest.exp (4 ms) 27: [ RUN ] SimdMathTest.expUnsafe 27: [ OK ] SimdMathTest.expUnsafe (1 ms) 27: [ RUN ] SimdMathTest.pow 27: [ OK ] SimdMathTest.pow (0 ms) 27: [ RUN ] SimdMathTest.powUnsafe 27: [ OK ] SimdMathTest.powUnsafe (0 ms) 27: [ RUN ] SimdMathTest.erf 27: [ OK ] SimdMathTest.erf (1 ms) 27: [ RUN ] SimdMathTest.erfc 27: [ OK ] SimdMathTest.erfc (1 ms) 27: [ RUN ] SimdMathTest.sin 27: [ OK ] SimdMathTest.sin (2 ms) 27: [ RUN ] SimdMathTest.cos 27: [ OK ] SimdMathTest.cos (1 ms) 27: [ RUN ] SimdMathTest.tan 27: [ OK ] SimdMathTest.tan (3 ms) 27: [ RUN ] SimdMathTest.asin 27: [ OK ] SimdMathTest.asin (0 ms) 27: [ RUN ] SimdMathTest.acos 27: [ OK ] SimdMathTest.acos (1 ms) 27: [ RUN ] SimdMathTest.atan 27: [ OK ] SimdMathTest.atan (1 ms) 27: [ RUN ] SimdMathTest.atan2 27: [ OK ] SimdMathTest.atan2 (0 ms) 27: [ RUN ] SimdMathTest.pmeForceCorrection 27: [ OK ] SimdMathTest.pmeForceCorrection (2 ms) 27: [ RUN ] SimdMathTest.pmePotentialCorrection 27: [ OK ] SimdMathTest.pmePotentialCorrection (1 ms) 27: [ RUN ] SimdMathTest.invsqrtSingleAccuracy 27: [ OK ] SimdMathTest.invsqrtSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy 27: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (18 ms) 27: [ RUN ] SimdMathTest.sqrtSingleAccuracy 27: [ OK ] SimdMathTest.sqrtSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe 27: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (1 ms) 27: [ RUN ] SimdMathTest.invSingleAccuracy 27: [ OK ] SimdMathTest.invSingleAccuracy (2 ms) 27: [ RUN ] SimdMathTest.cbrtSingleAccuracy 27: [ OK ] SimdMathTest.cbrtSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.invcbrtSingleAccuracy 27: [ OK ] SimdMathTest.invcbrtSingleAccuracy (3 ms) 27: [ RUN ] SimdMathTest.log2SingleAccuracy 27: [ OK ] SimdMathTest.log2SingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.logSingleAccuracy 27: [ OK ] SimdMathTest.logSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.exp2SingleAccuracy 27: [ OK ] SimdMathTest.exp2SingleAccuracy (2 ms) 27: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 27: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (1 ms) 27: [ RUN ] SimdMathTest.expSingleAccuracy 27: [ OK ] SimdMathTest.expSingleAccuracy (3 ms) 27: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe 27: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (0 ms) 27: [ RUN ] SimdMathTest.powSingleAccuracy 27: [ OK ] SimdMathTest.powSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.powSingleAccuracyUnsafe 27: [ OK ] SimdMathTest.powSingleAccuracyUnsafe (0 ms) 27: [ RUN ] SimdMathTest.erfSingleAccuracy 27: [ OK ] SimdMathTest.erfSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.erfcSingleAccuracy 27: [ OK ] SimdMathTest.erfcSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.sinSingleAccuracy 27: [ OK ] SimdMathTest.sinSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.cosSingleAccuracy 27: [ OK ] SimdMathTest.cosSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.tanSingleAccuracy 27: [ OK ] SimdMathTest.tanSingleAccuracy (2 ms) 27: [ RUN ] SimdMathTest.asinSingleAccuracy 27: [ OK ] SimdMathTest.asinSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.acosSingleAccuracy 27: [ OK ] SimdMathTest.acosSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.atanSingleAccuracy 27: [ OK ] SimdMathTest.atanSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.atan2SingleAccuracy 27: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy 27: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 27: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (1 ms) 27: [----------] 56 tests from SimdMathTest (81 ms total) 27: 27: [----------] 1 test from EmptyArrayRefTest 27: [ RUN ] EmptyArrayRefTest.IsEmpty 27: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 27: [----------] 1 test from EmptyArrayRefTest (0 ms total) 27: 27: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 27: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 27: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks 27: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) 27: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks 27: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) 27: [----------] 3 tests from ArrayRefTest/0 (0 ms total) 27: 27: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 27: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 27: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks 27: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) 27: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks 27: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) 27: [----------] 3 tests from ArrayRefTest/1 (0 ms total) 27: 27: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 27: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 27: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks 27: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) 27: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks 27: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) 27: [----------] 3 tests from ArrayRefTest/2 (0 ms total) 27: 27: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 27: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 27: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks 27: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) 27: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks 27: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) 27: [----------] 3 tests from ArrayRefTest/3 (0 ms total) 27: 27: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefReadWriteTest/0.Assignment 27: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) 27: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) 27: 27: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefReadWriteTest/1.Assignment 27: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) 27: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) 27: 27: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefArithmeticTest/0.Basic 27: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) 27: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) 27: 27: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefArithmeticTest/1.Basic 27: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) 27: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) 27: 27: [----------] 23 tests from SimdIntegerTest 27: [ RUN ] SimdIntegerTest.setZero 27: [ OK ] SimdIntegerTest.setZero (0 ms) 27: [ RUN ] SimdIntegerTest.set 27: [ OK ] SimdIntegerTest.set (0 ms) 27: [ RUN ] SimdIntegerTest.add 27: [ OK ] SimdIntegerTest.add (0 ms) 27: [ RUN ] SimdIntegerTest.sub 27: [ OK ] SimdIntegerTest.sub (0 ms) 27: [ RUN ] SimdIntegerTest.mul 27: [ OK ] SimdIntegerTest.mul (0 ms) 27: [ RUN ] SimdIntegerTest.and 27: [ OK ] SimdIntegerTest.and (0 ms) 27: [ RUN ] SimdIntegerTest.andNot 27: [ OK ] SimdIntegerTest.andNot (0 ms) 27: [ RUN ] SimdIntegerTest.or 27: [ OK ] SimdIntegerTest.or (0 ms) 27: [ RUN ] SimdIntegerTest.xor 27: [ OK ] SimdIntegerTest.xor (0 ms) 27: [ RUN ] SimdIntegerTest.extract 27: [ OK ] SimdIntegerTest.extract (0 ms) 27: [ RUN ] SimdIntegerTest.cvtR2I 27: [ OK ] SimdIntegerTest.cvtR2I (0 ms) 27: [ RUN ] SimdIntegerTest.cvttR2I 27: [ OK ] SimdIntegerTest.cvttR2I (0 ms) 27: [ RUN ] SimdIntegerTest.cvtI2R 27: [ OK ] SimdIntegerTest.cvtI2R (0 ms) 27: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask 27: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) 27: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask 27: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) 27: [ RUN ] SimdIntegerTest.cmpLt 27: [ OK ] SimdIntegerTest.cmpLt (0 ms) 27: [ RUN ] SimdIntegerTest.testBits 27: [ OK ] SimdIntegerTest.testBits (0 ms) 27: [ RUN ] SimdIntegerTest.andB 27: [ OK ] SimdIntegerTest.andB (0 ms) 27: [ RUN ] SimdIntegerTest.orB 27: [ OK ] SimdIntegerTest.orB (0 ms) 27: [ RUN ] SimdIntegerTest.anyTrue 27: [ OK ] SimdIntegerTest.anyTrue (0 ms) 27: [ RUN ] SimdIntegerTest.blend 27: [ OK ] SimdIntegerTest.blend (0 ms) 27: [ RUN ] SimdIntegerTest.cvtB2IB 27: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) 27: [ RUN ] SimdIntegerTest.cvtIB2B 27: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) 27: [----------] 23 tests from SimdIntegerTest (1 ms total) 27: 27: [----------] 41 tests from SimdScalarTest 27: [ RUN ] SimdScalarTest.load 27: [ OK ] SimdScalarTest.load (0 ms) 27: [ RUN ] SimdScalarTest.loadU 27: [ OK ] SimdScalarTest.loadU (0 ms) 27: [ RUN ] SimdScalarTest.store 27: [ OK ] SimdScalarTest.store (0 ms) 27: [ RUN ] SimdScalarTest.storeU 27: [ OK ] SimdScalarTest.storeU (0 ms) 27: [ RUN ] SimdScalarTest.setZero 27: [ OK ] SimdScalarTest.setZero (0 ms) 27: [ RUN ] SimdScalarTest.andNot 27: [ OK ] SimdScalarTest.andNot (0 ms) 27: [ RUN ] SimdScalarTest.fma 27: [ OK ] SimdScalarTest.fma (0 ms) 27: [ RUN ] SimdScalarTest.fms 27: [ OK ] SimdScalarTest.fms (0 ms) 27: [ RUN ] SimdScalarTest.fnma 27: [ OK ] SimdScalarTest.fnma (0 ms) 27: [ RUN ] SimdScalarTest.fnms 27: [ OK ] SimdScalarTest.fnms (0 ms) 27: [ RUN ] SimdScalarTest.maskAdd 27: [ OK ] SimdScalarTest.maskAdd (0 ms) 27: [ RUN ] SimdScalarTest.maskzMul 27: [ OK ] SimdScalarTest.maskzMul (0 ms) 27: [ RUN ] SimdScalarTest.maskzFma 27: [ OK ] SimdScalarTest.maskzFma (0 ms) 27: [ RUN ] SimdScalarTest.abs 27: [ OK ] SimdScalarTest.abs (0 ms) 27: [ RUN ] SimdScalarTest.max 27: [ OK ] SimdScalarTest.max (0 ms) 27: [ RUN ] SimdScalarTest.min 27: [ OK ] SimdScalarTest.min (0 ms) 27: [ RUN ] SimdScalarTest.round 27: [ OK ] SimdScalarTest.round (0 ms) 27: [ RUN ] SimdScalarTest.trunc 27: [ OK ] SimdScalarTest.trunc (0 ms) 27: [ RUN ] SimdScalarTest.reduce 27: [ OK ] SimdScalarTest.reduce (0 ms) 27: [ RUN ] SimdScalarTest.testBits 27: [ OK ] SimdScalarTest.testBits (0 ms) 27: [ RUN ] SimdScalarTest.anyTrue 27: [ OK ] SimdScalarTest.anyTrue (0 ms) 27: [ RUN ] SimdScalarTest.selectByMask 27: [ OK ] SimdScalarTest.selectByMask (0 ms) 27: [ RUN ] SimdScalarTest.selectByNotMask 27: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 27: [ RUN ] SimdScalarTest.blend 27: [ OK ] SimdScalarTest.blend (0 ms) 27: [ RUN ] SimdScalarTest.cvtR2I 27: [ OK ] SimdScalarTest.cvtR2I (0 ms) 27: [ RUN ] SimdScalarTest.cvttR2I 27: [ OK ] SimdScalarTest.cvttR2I (0 ms) 27: [ RUN ] SimdScalarTest.cvtI2R 27: [ OK ] SimdScalarTest.cvtI2R (0 ms) 27: [ RUN ] SimdScalarTest.cvtF2D 27: [ OK ] SimdScalarTest.cvtF2D (0 ms) 27: [ RUN ] SimdScalarTest.cvtD2D 27: [ OK ] SimdScalarTest.cvtD2D (0 ms) 27: [ RUN ] SimdScalarTest.loadI 27: [ OK ] SimdScalarTest.loadI (0 ms) 27: [ RUN ] SimdScalarTest.loadUI 27: [ OK ] SimdScalarTest.loadUI (0 ms) 27: [ RUN ] SimdScalarTest.storeI 27: [ OK ] SimdScalarTest.storeI (0 ms) 27: [ RUN ] SimdScalarTest.storeUI 27: [ OK ] SimdScalarTest.storeUI (0 ms) 27: [ RUN ] SimdScalarTest.andNotI 27: [ OK ] SimdScalarTest.andNotI (0 ms) 27: [ RUN ] SimdScalarTest.testBitsI 27: [ OK ] SimdScalarTest.testBitsI (0 ms) 27: [ RUN ] SimdScalarTest.selectByMaskI 27: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 27: [ RUN ] SimdScalarTest.selectByNotMaskI 27: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 27: [ RUN ] SimdScalarTest.blendI 27: [ OK ] SimdScalarTest.blendI (0 ms) 27: [ RUN ] SimdScalarTest.cvtB2IB 27: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 27: [ RUN ] SimdScalarTest.cvtIB2B 27: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 27: [ RUN ] SimdScalarTest.expandScalarsToTriplets 27: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 27: [----------] 41 tests from SimdScalarTest (0 ms total) 27: 27: [----------] 8 tests from SimdScalarUtilTest 27: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 27: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 27: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 27: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 27: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 27: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 27: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 27: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 27: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 27: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 27: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 27: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 27: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 27: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 27: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 27: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 27: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 27: 27: [----------] 37 tests from SimdScalarMathTest 27: [ RUN ] SimdScalarMathTest.copysign 27: [ OK ] SimdScalarMathTest.copysign (0 ms) 27: [ RUN ] SimdScalarMathTest.invsqrtPair 27: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 27: [ RUN ] SimdScalarMathTest.inv 27: [ OK ] SimdScalarMathTest.inv (0 ms) 27: [ RUN ] SimdScalarMathTest.maskzInvsqrt 27: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 27: [ RUN ] SimdScalarMathTest.log 27: [ OK ] SimdScalarMathTest.log (0 ms) 27: [ RUN ] SimdScalarMathTest.exp2 27: [ OK ] SimdScalarMathTest.exp2 (0 ms) 27: [ RUN ] SimdScalarMathTest.exp 27: [ OK ] SimdScalarMathTest.exp (0 ms) 27: [ RUN ] SimdScalarMathTest.erf 27: [ OK ] SimdScalarMathTest.erf (0 ms) 27: [ RUN ] SimdScalarMathTest.erfc 27: [ OK ] SimdScalarMathTest.erfc (0 ms) 27: [ RUN ] SimdScalarMathTest.sincos 27: [ OK ] SimdScalarMathTest.sincos (0 ms) 27: [ RUN ] SimdScalarMathTest.sin 27: [ OK ] SimdScalarMathTest.sin (0 ms) 27: [ RUN ] SimdScalarMathTest.cos 27: [ OK ] SimdScalarMathTest.cos (0 ms) 27: [ RUN ] SimdScalarMathTest.tan 27: [ OK ] SimdScalarMathTest.tan (0 ms) 27: [ RUN ] SimdScalarMathTest.asin 27: [ OK ] SimdScalarMathTest.asin (0 ms) 27: [ RUN ] SimdScalarMathTest.acos 27: [ OK ] SimdScalarMathTest.acos (0 ms) 27: [ RUN ] SimdScalarMathTest.atan 27: [ OK ] SimdScalarMathTest.atan (0 ms) 27: [ RUN ] SimdScalarMathTest.atan2 27: [ OK ] SimdScalarMathTest.atan2 (0 ms) 27: [ RUN ] SimdScalarMathTest.pmeForceCorrection 27: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 27: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 27: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 27: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 27: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.invSingleAccuracy 27: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 27: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.logSingleAccuracy 27: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 27: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.expSingleAccuracy 27: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 27: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 27: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 27: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 27: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 27: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 27: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 27: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 27: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 27: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 27: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 27: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 27: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 27: [----------] 37 tests from SimdScalarMathTest (1 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 247 tests from 19 test cases ran. (83 ms total) 27: [ PASSED ] 247 tests. 27/54 Test #27: SimdUnitTests ....................... Passed 0.10 sec test 28 Start 28: CompatibilityHelpersTests 28: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/compat-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/CompatibilityHelpersTests.xml" 28: Test timeout computed to be: 30 28: [==========] Running 170 tests from 12 test cases. 28: [----------] Global test environment set-up. 28: [----------] 45 tests from OptionalTest 28: [ RUN ] OptionalTest.UnionCanContainNonPodTypes 28: [ OK ] OptionalTest.UnionCanContainNonPodTypes (0 ms) 28: [ RUN ] OptionalTest.CanDefaultConstructEmpty 28: [ OK ] OptionalTest.CanDefaultConstructEmpty (0 ms) 28: [ RUN ] OptionalTest.CanConstructFromNullopt 28: [ OK ] OptionalTest.CanConstructFromNullopt (0 ms) 28: [ RUN ] OptionalTest.CanDefaultConstructUsingNonDefaultConstructibleType 28: [ OK ] OptionalTest.CanDefaultConstructUsingNonDefaultConstructibleType (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptional 28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptional (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptional 28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptional (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptionalWithExplicitConversion 28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptionalWithExplicitConversion (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptionalNonExplicitConverting 28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptionalNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptionalExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptionalExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptionalNonExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptionalNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptional 28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptional (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptionalExplicitConverting 28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptionalExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptionalNonExplicitConverting 28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptionalNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptional 28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptional (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptionalExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptionalExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptionalNonExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptionalNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromLiteral 28: [ OK ] OptionalTest.CanCopyConstructFromLiteral (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromLiteralConverting 28: [ OK ] OptionalTest.CanCopyConstructFromLiteralConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromValue 28: [ OK ] OptionalTest.CanCopyConstructFromValue (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromValueConverting 28: [ OK ] OptionalTest.CanCopyConstructFromValueConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromValue 28: [ OK ] OptionalTest.CanMoveConstructFromValue (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromValueExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromValueExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromValueNonExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromValueNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceConstructFromLiteral 28: [ OK ] OptionalTest.CanInPlaceConstructFromLiteral (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceCopyConstructFromValue 28: [ OK ] OptionalTest.CanInPlaceCopyConstructFromValue (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceMoveConstructFromValue 28: [ OK ] OptionalTest.CanInPlaceMoveConstructFromValue (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceCopyConstructFromInitializerList 28: [ OK ] OptionalTest.CanInPlaceCopyConstructFromInitializerList (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceMoveConstructFromInitializerList 28: [ OK ] OptionalTest.CanInPlaceMoveConstructFromInitializerList (0 ms) 28: [ RUN ] OptionalTest.CanAssignNulloptToDisengage 28: [ OK ] OptionalTest.CanAssignNulloptToDisengage (0 ms) 28: [ RUN ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionals 28: [ OK ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionals (0 ms) 28: [ RUN ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionalsConverting 28: [ OK ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionalsConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionalsConverting 28: [ OK ] OptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionalsConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyAssignFromLiteral 28: [ OK ] OptionalTest.CanCopyAssignFromLiteral (0 ms) 28: [ RUN ] OptionalTest.CanCopyAssignFromValue 28: [ OK ] OptionalTest.CanCopyAssignFromValue (0 ms) 28: [ RUN ] OptionalTest.CanMoveAssignFromValue 28: [ OK ] OptionalTest.CanMoveAssignFromValue (0 ms) 28: [ RUN ] OptionalTest.CanCopyEmplaceFromArguments 28: [ OK ] OptionalTest.CanCopyEmplaceFromArguments (0 ms) 28: [ RUN ] OptionalTest.CanMoveEmplaceFromArguments 28: [ OK ] OptionalTest.CanMoveEmplaceFromArguments (0 ms) 28: [ RUN ] OptionalTest.CanCopyEmplaceFromInitializerListAndArguments 28: [ OK ] OptionalTest.CanCopyEmplaceFromInitializerListAndArguments (0 ms) 28: [ RUN ] OptionalTest.CanMoveEmplaceFromInitializerListAndArguments 28: [ OK ] OptionalTest.CanMoveEmplaceFromInitializerListAndArguments (0 ms) 28: [ RUN ] OptionalTest.CanResetContent 28: [ OK ] OptionalTest.CanResetContent (0 ms) 28: [ RUN ] OptionalTest.ProvidesRelationalOperators 28: [ OK ] OptionalTest.ProvidesRelationalOperators (0 ms) 28: [ RUN ] OptionalTest.ProvidesMixedTypeRelationalOperators 28: [ OK ] OptionalTest.ProvidesMixedTypeRelationalOperators (1 ms) 28: [ RUN ] OptionalTest.CanProduceHash 28: [ OK ] OptionalTest.CanProduceHash (0 ms) 28: [ RUN ] OptionalTest.ShowAlignmentDependingOnBaseType 28: alignment_of: 1 28: alignment_of: 2 28: alignment_of: 4 28: alignment_of: 8 28: alignment_of: 4 28: alignment_of: 8 28: alignment_of: 16 28: alignment_of: 1 28: [ OK ] OptionalTest.ShowAlignmentDependingOnBaseType (0 ms) 28: [ RUN ] OptionalTest.ShowSizeDependingOnBaseType 28: sizeof( nonstd::optional_lite::detail::storage_t ): 1 28: sizeof( optional ): 2 (1) 28: sizeof( optional ): 4 (2) 28: sizeof( optional ): 8 (4) 28: sizeof( optional ): 16 (8) 28: sizeof( optional ): 8 (4) 28: sizeof( optional ): 16 (8) 28: sizeof( optional ): 32 (16) 28: sizeof( optional ): 2 (1) 28: [ OK ] OptionalTest.ShowSizeDependingOnBaseType (0 ms) 28: [----------] 45 tests from OptionalTest (1 ms total) 28: 28: [----------] 7 tests from MakeOptionalTest 28: [ RUN ] MakeOptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionals 28: [ OK ] MakeOptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionals (0 ms) 28: [ RUN ] MakeOptionalTest.CanCopyConstruct 28: [ OK ] MakeOptionalTest.CanCopyConstruct (0 ms) 28: [ RUN ] MakeOptionalTest.CanMoveConstruct 28: [ OK ] MakeOptionalTest.CanMoveConstruct (0 ms) 28: [ RUN ] MakeOptionalTest.CanInPlaceCopyConstructFromArguments 28: [ OK ] MakeOptionalTest.CanInPlaceCopyConstructFromArguments (0 ms) 28: [ RUN ] MakeOptionalTest.CanInPlaceMoveConstructFromArguments 28: [ OK ] MakeOptionalTest.CanInPlaceMoveConstructFromArguments (0 ms) 28: [ RUN ] MakeOptionalTest.CanInPlaceCopyConstructFromInitializerListAndArguments 28: [ OK ] MakeOptionalTest.CanInPlaceCopyConstructFromInitializerListAndArguments (0 ms) 28: [ RUN ] MakeOptionalTest.CanInPlaceMoveConstructFromInitializerListAndArguments 28: [ OK ] MakeOptionalTest.CanInPlaceMoveConstructFromInitializerListAndArguments (0 ms) 28: [----------] 7 tests from MakeOptionalTest (0 ms total) 28: 28: [----------] 4 tests from OptionalMemberSwapTest 28: [ RUN ] OptionalMemberSwapTest.CanSwapDisengagedWithDisengaged 28: [ OK ] OptionalMemberSwapTest.CanSwapDisengagedWithDisengaged (0 ms) 28: [ RUN ] OptionalMemberSwapTest.CanSwapEngagedWithDisengaged 28: [ OK ] OptionalMemberSwapTest.CanSwapEngagedWithDisengaged (0 ms) 28: [ RUN ] OptionalMemberSwapTest.CanSwapDisengagedWithEngaged 28: [ OK ] OptionalMemberSwapTest.CanSwapDisengagedWithEngaged (0 ms) 28: [ RUN ] OptionalMemberSwapTest.CanSwapEngagedWithEngaged 28: [ OK ] OptionalMemberSwapTest.CanSwapEngagedWithEngaged (0 ms) 28: [----------] 4 tests from OptionalMemberSwapTest (0 ms total) 28: 28: [----------] 4 tests from OptionalImplicitValueTest 28: [ RUN ] OptionalImplicitValueTest.CanObtainValueConst 28: [ OK ] OptionalImplicitValueTest.CanObtainValueConst (0 ms) 28: [ RUN ] OptionalImplicitValueTest.CanObtainValueNonConst 28: [ OK ] OptionalImplicitValueTest.CanObtainValueNonConst (0 ms) 28: [ RUN ] OptionalImplicitValueTest.CanObtainMovedFromValueConst 28: [ OK ] OptionalImplicitValueTest.CanObtainMovedFromValueConst (0 ms) 28: [ RUN ] OptionalImplicitValueTest.CanObtainMovedFromValueNonConst 28: [ OK ] OptionalImplicitValueTest.CanObtainMovedFromValueNonConst (0 ms) 28: [----------] 4 tests from OptionalImplicitValueTest (0 ms total) 28: 28: [----------] 20 tests from OptionalIntValueTest 28: [ RUN ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorConst 28: [ OK ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorNonConst 28: [ OK ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorNonConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorConst 28: [ OK ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorNonConst 28: [ OK ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorNonConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainHasValueViaOperatorBool 28: [ OK ] OptionalIntValueTest.CanObtainHasValueViaOperatorBool (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainValueViaValueMethodConst 28: [ OK ] OptionalIntValueTest.CanObtainValueViaValueMethodConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainValueViaValueMethodNonConst 28: [ OK ] OptionalIntValueTest.CanObtainValueViaValueMethodNonConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodConst 28: [ OK ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodNonConst 28: [ OK ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodNonConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainValueFromNonEmptyOptionalViaValueOrMethod 28: [ OK ] OptionalIntValueTest.CanObtainValueFromNonEmptyOptionalViaValueOrMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainDefaultFromEmptyOptionalViaValueOrMethod 28: [ OK ] OptionalIntValueTest.CanObtainDefaultFromEmptyOptionalViaValueOrMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedFromValueForLValuesViaValueOrMethod 28: [ OK ] OptionalIntValueTest.CanObtainMovedFromValueForLValuesViaValueOrMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedFromValueForRValuesViaValueOrMethod 28: [ OK ] OptionalIntValueTest.CanObtainMovedFromValueForRValuesViaValueOrMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForLValues 28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForLValues (0 ms) 28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForRValues 28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForRValues (0 ms) 28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessWithNonEmptyWhatMethod 28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessWithNonEmptyWhatMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithDisengaged 28: [ OK ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithDisengaged (0 ms) 28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithEngaged 28: [ OK ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithEngaged (0 ms) 28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithEngaged 28: [ OK ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithEngaged (0 ms) 28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithDisengaged 28: [ OK ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithDisengaged (0 ms) 28: [----------] 20 tests from OptionalIntValueTest (0 ms total) 28: 28: [----------] 1 test from NotNullConstruction 28: [ RUN ] NotNullConstruction.Works 28: [ OK ] NotNullConstruction.Works (0 ms) 28: [----------] 1 test from NotNullConstruction (0 ms total) 28: 28: [----------] 1 test from NotNullCasting 28: [ RUN ] NotNullCasting.Works 28: [ OK ] NotNullCasting.Works (0 ms) 28: [----------] 1 test from NotNullCasting (0 ms total) 28: 28: [----------] 1 test from NotNullAssignment 28: [ RUN ] NotNullAssignment.Works 28: [ OK ] NotNullAssignment.Works (0 ms) 28: [----------] 1 test from NotNullAssignment (0 ms total) 28: 28: [----------] 1 test from MakeNotNull 28: [ RUN ] MakeNotNull.Works 28: [ OK ] MakeNotNull.Works (0 ms) 28: [----------] 1 test from MakeNotNull (0 ms total) 28: 28: [----------] 1 test from NotNull 28: [ RUN ] NotNull.WorksInContainers 28: [ OK ] NotNull.WorksInContainers (0 ms) 28: [----------] 1 test from NotNull (0 ms total) 28: 28: [----------] 80 tests from StringViewTest 28: [ RUN ] StringViewTest.CanDefaultConstructEmptyView 28: [ OK ] StringViewTest.CanDefaultConstructEmptyView (0 ms) 28: [ RUN ] StringViewTest.CanConstructFromPointerAndSize 28: [ OK ] StringViewTest.CanConstructFromPointerAndSize (0 ms) 28: [ RUN ] StringViewTest.CanConstructFromCString 28: [ OK ] StringViewTest.CanConstructFromCString (0 ms) 28: [ RUN ] StringViewTest.CanCopyConstructFromEmptyView 28: [ OK ] StringViewTest.CanCopyConstructFromEmptyView (0 ms) 28: [ RUN ] StringViewTest.CanCopyConstructFromNonEmptyView 28: [ OK ] StringViewTest.CanCopyConstructFromNonEmptyView (0 ms) 28: [ RUN ] StringViewTest.CanCopyAssingFromEmptyView 28: [ OK ] StringViewTest.CanCopyAssingFromEmptyView (0 ms) 28: [ RUN ] StringViewTest.CanCopyAssingFromNonEmptyView 28: [ OK ] StringViewTest.CanCopyAssingFromNonEmptyView (0 ms) 28: [ RUN ] StringViewTest.AllowForwardIteration 28: [ OK ] StringViewTest.AllowForwardIteration (0 ms) 28: [ RUN ] StringViewTest.AllowConstForwardIteration 28: [ OK ] StringViewTest.AllowConstForwardIteration (0 ms) 28: [ RUN ] StringViewTest.AllowReverseIteration 28: [ OK ] StringViewTest.AllowReverseIteration (0 ms) 28: [ RUN ] StringViewTest.AllowConstReverseIteration 28: [ OK ] StringViewTest.AllowConstReverseIteration (0 ms) 28: [ RUN ] StringViewTest.CanObtainSizeFromViewViaSize 28: [ OK ] StringViewTest.CanObtainSizeFromViewViaSize (0 ms) 28: [ RUN ] StringViewTest.CanObtainSizeFromViewViaLength 28: [ OK ] StringViewTest.CanObtainSizeFromViewViaLength (0 ms) 28: [ RUN ] StringViewTest.CanObtainMaxSizeViaMaxSize 28: [ OK ] StringViewTest.CanObtainMaxSizeViaMaxSize (0 ms) 28: [ RUN ] StringViewTest.CanCheckForEmptyStringWithEmpty 28: [ OK ] StringViewTest.CanCheckForEmptyStringWithEmpty (0 ms) 28: [ RUN ] StringViewTest.CanAccessElementViaArrayIndex 28: [ OK ] StringViewTest.CanAccessElementViaArrayIndex (0 ms) 28: [ RUN ] StringViewTest.CanAccessElementViaAt 28: [ OK ] StringViewTest.CanAccessElementViaAt (0 ms) 28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsAccess 28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsAccess (0 ms) 28: [ RUN ] StringViewTest.CanAccessAllElementsViaData 28: [ OK ] StringViewTest.CanAccessAllElementsViaData (0 ms) 28: [ RUN ] StringViewTest.DataFromEmptyStringIsNullptr 28: [ OK ] StringViewTest.DataFromEmptyStringIsNullptr (0 ms) 28: [ RUN ] StringViewTest.CanRemovePrefix 28: [ OK ] StringViewTest.CanRemovePrefix (0 ms) 28: [ RUN ] StringViewTest.CanRemoveSuffix 28: [ OK ] StringViewTest.CanRemoveSuffix (0 ms) 28: [ RUN ] StringViewTest.CanSwapWithOtherView 28: [ OK ] StringViewTest.CanSwapWithOtherView (0 ms) 28: [ RUN ] StringViewTest.CanCopySubstringWithCopy 28: [ OK ] StringViewTest.CanCopySubstringWithCopy (0 ms) 28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsCopy 28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsCopy (0 ms) 28: [ RUN ] StringViewTest.CanObtainSubstringWithSubstr 28: [ OK ] StringViewTest.CanObtainSubstringWithSubstr (0 ms) 28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsSubstr 28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsSubstr (0 ms) 28: [ RUN ] StringViewTest.CanLexicallyCompareViewWithCompare 28: [ OK ] StringViewTest.CanLexicallyCompareViewWithCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareEmptyViewsWIthCompare 28: [ OK ] StringViewTest.CanCompareEmptyViewsWIthCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareSubStringWithViewViaCompare 28: [ OK ] StringViewTest.CanCompareSubStringWithViewViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareSubStringWithSubStringViewViaCompare 28: [ OK ] StringViewTest.CanCompareSubStringWithSubStringViewViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareToCStringViaCompare 28: [ OK ] StringViewTest.CanCompareToCStringViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareSubStringToCStringViaCompare 28: [ OK ] StringViewTest.CanCompareSubStringToCStringViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareSubStringToCStringPrefixViaCompare 28: [ OK ] StringViewTest.CanCompareSubStringToCStringPrefixViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCheckForPrefixViewViaStartsWith 28: [ OK ] StringViewTest.CanCheckForPrefixViewViaStartsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForPrefixCharacterViaStartsWith 28: [ OK ] StringViewTest.CanCheckForPrefixCharacterViaStartsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForPrefixCStringViaStartsWith 28: [ OK ] StringViewTest.CanCheckForPrefixCStringViaStartsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForSuffixViewViaEndsWith 28: [ OK ] StringViewTest.CanCheckForSuffixViewViaEndsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForSuffixCharacterViaEndsWith 28: [ OK ] StringViewTest.CanCheckForSuffixCharacterViaEndsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForSuffixCStringViaEndsWith 28: [ OK ] StringViewTest.CanCheckForSuffixCStringViaEndsWith (0 ms) 28: [ RUN ] StringViewTest.CanSearchForViewSubstrViaFind 28: [ OK ] StringViewTest.CanSearchForViewSubstrViaFind (0 ms) 28: [ RUN ] StringViewTest.CanSearchForCharacterViaFind 28: [ OK ] StringViewTest.CanSearchForCharacterViaFind (0 ms) 28: [ RUN ] StringViewTest.CanSearchForCStringSubstringViaFind 28: [ OK ] StringViewTest.CanSearchForCStringSubstringViaFind (0 ms) 28: [ RUN ] StringViewTest.CanSearchForCStringSubstringViaFindWithDefaultPos 28: [ OK ] StringViewTest.CanSearchForCStringSubstringViaFindWithDefaultPos (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForViewSubstrViaFind 28: [ OK ] StringViewTest.CanBackwardsSearchForViewSubstrViaFind (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForCharacterViaFind 28: [ OK ] StringViewTest.CanBackwardsSearchForCharacterViaFind (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFind 28: [ OK ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFind (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFindWithDefaultPos 28: [ OK ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFindWithDefaultPos (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfAnyCharacterInView 28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfAnyCharacterInView (1 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharacter 28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharacter (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCStringInLenght 28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCStringInLenght (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCString 28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCString (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfAnyCharacterInView 28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfAnyCharacterInView (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharacter 28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharacter (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCStringInLenght 28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCStringInLenght (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCString 28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCString (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstNotFoundCharacter 28: [ OK ] StringViewTest.CanSearchForFirstNotFoundCharacter (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstNonMatchingCharacter 28: [ OK ] StringViewTest.CanSearchForFirstNonMatchingCharacter (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCStringInLength 28: [ OK ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCStringInLength (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCString 28: [ OK ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCString (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForForstNonFoundCharacterInView 28: [ OK ] StringViewTest.CanBackwardsSearchForForstNonFoundCharacterInView (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonMatchingCharacter 28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonMatchingCharacter (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCStringInLength 28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCStringInLength (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCString 28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCString (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSV 28: [ OK ] StringViewTest.CanCreateViewWithLiteralSV (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsStringViewLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsStringViewLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInStringViewLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInStringViewLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SV 28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SV (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsStringViewLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsStringViewLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInStringViewLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInStringViewLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCompareToViews 28: [ OK ] StringViewTest.CanCompareToViews (0 ms) 28: [ RUN ] StringViewTest.CanCompareViewToImplicitlyConvertedView 28: [ OK ] StringViewTest.CanCompareViewToImplicitlyConvertedView (0 ms) 28: [ RUN ] StringViewTest.EmptyViewsCompareAsEqual 28: [ OK ] StringViewTest.EmptyViewsCompareAsEqual (0 ms) 28: [ RUN ] StringViewTest.CanPrintViewToPutputStream 28: [ OK ] StringViewTest.CanPrintViewToPutputStream (0 ms) 28: [ RUN ] StringViewTest.HashOfViewIsEqualToHashOfString 28: [ OK ] StringViewTest.HashOfViewIsEqualToHashOfString (0 ms) 28: [ RUN ] StringViewTest.HashOfWStringViewIsEqualToHashOfString 28: [ OK ] StringViewTest.HashOfWStringViewIsEqualToHashOfString (0 ms) 28: [ RUN ] StringViewTest.HashOfU16StringViewIsEqualToHashOfString 28: [ OK ] StringViewTest.HashOfU16StringViewIsEqualToHashOfString (0 ms) 28: [ RUN ] StringViewTest.HashOfU32StringViewIsEqualToHashOfString 28: [ OK ] StringViewTest.HashOfU32StringViewIsEqualToHashOfString (0 ms) 28: [----------] 80 tests from StringViewTest (1 ms total) 28: 28: [----------] 5 tests from StringViewExtensionTest 28: [ RUN ] StringViewExtensionTest.CanConstructViewFromString 28: [ OK ] StringViewExtensionTest.CanConstructViewFromString (0 ms) 28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaExplicitOperator 28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaExplicitOperator (0 ms) 28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaToString 28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaToString (0 ms) 28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaToStringFreeFunction 28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaToStringFreeFunction (0 ms) 28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViewViaToStringView 28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViewViaToStringView (0 ms) 28: [----------] 5 tests from StringViewExtensionTest (0 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 170 tests from 12 test cases ran. (3 ms total) 28: [ PASSED ] 170 tests. 28/54 Test #28: CompatibilityHelpersTests ........... Passed 0.02 sec test 29 Start 29: GmxAnaTest 29: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/gmxana-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/GmxAnaTest.xml" 29: Test timeout computed to be: 600 29: [==========] Running 27 tests from 5 test cases. 29: [----------] Global test environment set-up. 29: [----------] 5 tests from Entropy 29: [ RUN ] Entropy.Schlitter_300_NoLinear 29: [ OK ] Entropy.Schlitter_300_NoLinear (0 ms) 29: [ RUN ] Entropy.Schlitter_300_Linear 29: [ OK ] Entropy.Schlitter_300_Linear (0 ms) 29: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear 29: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms) 29: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear 29: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms) 29: [ RUN ] Entropy.QuasiHarmonic_200_Linear 29: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms) 29: [----------] 5 tests from Entropy (0 ms total) 29: 29: [----------] 10 tests from MindistTest 29: [ RUN ] MindistTest.mindistWorksWithSingleAtoms 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 0: 'atom1' 29: Selected 1: 'atom2' 29: [ OK ] MindistTest.mindistWorksWithSingleAtoms (2 ms) 29: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 2: 'atom3' 29: Selected 3: 'atoms12' 29: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (1 ms) 29: [ RUN ] MindistTest.mindistDoesNotPickUpContacts 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 0: 'atom1' 29: Selected 1: 'atom2' 29: [ OK ] MindistTest.mindistDoesNotPickUpContacts (3 ms) 29: [ RUN ] MindistTest.mindistPicksUpContacts 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 0: 'atom1' 29: Selected 1: 'atom2' 29: [ OK ] MindistTest.mindistPicksUpContacts (1 ms) 29: [ RUN ] MindistTest.ngWorks 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 0: 'atom1' 29: Selected 1: 'atom2' 29: Selected 2: 'atom3' 29: [ OK ] MindistTest.ngWorks (1 ms) 29: [ RUN ] MindistTest.groupWorks 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 3: 'atoms12' 29: Selected 2: 'atom3' 29: [ OK ] MindistTest.groupWorks (1 ms) 29: [ RUN ] MindistTest.maxDistWorks 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 2: 'atom3' 29: Selected 3: 'atoms12' 29: [ OK ] MindistTest.maxDistWorks (1 ms) 29: [ RUN ] MindistTest.noPbcWorks 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 0: 'atom1' 29: Selected 1: 'atom2' 29: [ OK ] MindistTest.noPbcWorks (1 ms) 29: [ RUN ] MindistTest.resPerTimeWorks 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 3: 'atoms12' 29: Selected 2: 'atom3' 29: [ OK ] MindistTest.resPerTimeWorks (2 ms) 29: [ RUN ] MindistTest.matrixWorks 29: Group 0 ( atom1) has 1 elements 29: Group 1 ( atom2) has 1 elements 29: Group 2 ( atom3) has 1 elements 29: Group 3 ( atoms12) has 2 elements 29: Group 4 ( atoms23) has 2 elements 29: Group 5 ( atoms123) has 3 elements 29: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 29: Reading frame 0 time 0.000 Last frame 0 time 0.000 29: Selected 5: 'atoms123' 29: Special case: making distance matrix between all atoms in group atoms123 29: [ OK ] MindistTest.matrixWorks (1 ms) 29: [----------] 10 tests from MindistTest (15 ms total) 29: 29: [----------] 3 tests from MsdTest 29: [ RUN ] MsdTest.threeDimensionalDiffusion 29: 29: Select a group to calculate mean squared displacement for: 29: Group 0 ( particles) has 3 elements 29: There is one group in the index 29: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 29: 29: Used 1 restart points spaced 200 ps over 9 ps 29: 29: Fitting from 1 to 8 ps 29: 29: D[ particles] 4.0000 (+/- 0.0000) 1e-5 cm^2/s 29: [ OK ] MsdTest.threeDimensionalDiffusion (1 ms) 29: [ RUN ] MsdTest.twoDimensionalDiffusion 29: 29: Select a group to calculate mean squared displacement for: 29: Group 0 ( particles) has 3 elements 29: There is one group in the index 29: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 29: 29: Used 1 restart points spaced 200 ps over 9 ps 29: 29: Fitting from 1 to 8 ps 29: 29: D[ particles] 6.0000 (+/- 0.0000) 1e-5 cm^2/s 29: [ OK ] MsdTest.twoDimensionalDiffusion (1 ms) 29: [ RUN ] MsdTest.oneDimensionalDiffusion 29: 29: Select a group to calculate mean squared displacement for: 29: Group 0 ( particles) has 3 elements 29: There is one group in the index 29: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 29: 29: Used 1 restart points spaced 200 ps over 9 ps 29: 29: Fitting from 1 to 8 ps 29: 29: D[ particles] 8.0000 (+/- 0.0000) 1e-5 cm^2/s 29: [ OK ] MsdTest.oneDimensionalDiffusion (1 ms) 29: [----------] 3 tests from MsdTest (3 ms total) 29: 29: [----------] 3 tests from MsdMolTest 29: [ RUN ] MsdMolTest.diffMolMassWeighted 29: 29: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]: 29: For a correct single-point energy evaluation with nsteps = 0, use 29: continuation = yes to avoid constraining the input coordinates. 29: 29: Setting the LD random seed to -185598997 29: Generated 330891 of the 330891 non-bonded parameter combinations 29: Generating 1-4 interactions: fudge = 0.5 29: Generated 330891 of the 330891 1-4 parameter combinations 29: Excluding 2 bonded neighbours molecule type 'SOL' 29: Number of degrees of freedom in T-Coupling group rest is 27.00 29: 29: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]: 29: NVE simulation with an initial temperature of zero: will use a Verlet 29: buffer of 10%. Check your energy drift! 29: 29: 29: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]: 29: You are using a plain Coulomb cut-off, which might produce artifacts. 29: You might want to consider using PME electrostatics. 29: 29: 29: 29: There were 3 notes 29: Calculating diffusion coefficients for molecules. 29: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 29: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 29: 29: Select a group to calculate mean squared displacement for: 29: Group 0 ( water) has 15 elements 29: There is one group in the index 29: Split group of 15 atoms into 5 molecules 29: Reading frames from pdb file Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms 29: Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Reading frame 5 time 0.020 Reading frame 6 time 0.024 Reading frame 7 time 0.028 Reading frame 8 time 0.032 Reading frame 9 time 0.036 Reading frame 10 time 0.040 Reading frame 11 time 0.044 Reading frame 12 time 0.048 Reading frame 13 time 0.052 Reading frame 14 time 0.056 Reading frame 15 time 0.060 Reading frame 16 time 0.064 Reading frame 17 time 0.068 Reading frame 18 time 0.072 Reading frame 19 time 0.076 Reading frame 20 time 0.080 29: 29: Used 1 restart points spaced 200 ps over 0.1 ps 29: 29: This run will generate roughly 0 Mb of data 29: = 6.4731 Std. Dev. = 8.0969 Error = 3.6210 29: Fitting from 0.008 to 0.088 ps 29: 29: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s 29: [ OK ] MsdMolTest.diffMolMassWeighted (716 ms) 29: [ RUN ] MsdMolTest.diffMolNonMassWeighted 29: 29: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]: 29: For a correct single-point energy evaluation with nsteps = 0, use 29: continuation = yes to avoid constraining the input coordinates. 29: 29: Setting the LD random seed to -583536709 29: Generated 330891 of the 330891 non-bonded parameter combinations 29: Generating 1-4 interactions: fudge = 0.5 29: Generated 330891 of the 330891 1-4 parameter combinations 29: Excluding 2 bonded neighbours molecule type 'SOL' 29: Number of degrees of freedom in T-Coupling group rest is 27.00 29: 29: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]: 29: NVE simulation with an initial temperature of zero: will use a Verlet 29: buffer of 10%. Check your energy drift! 29: 29: 29: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]: 29: You are using a plain Coulomb cut-off, which might produce artifacts. 29: You might want to consider using PME electrostatics. 29: 29: 29: 29: There were 3 notes 29: Calculating diffusion coefficients for molecules. 29: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 29: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 29: 29: Select a group to calculate mean squared displacement for: 29: Group 0 ( water) has 15 elements 29: There is one group in the index 29: Split group of 15 atoms into 5 molecules 29: Reading frames from pdb file Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms 29: Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Reading frame 5 time 0.020 Reading frame 6 time 0.024 Reading frame 7 time 0.028 Reading frame 8 time 0.032 Reading frame 9 time 0.036 Reading frame 10 time 0.040 Reading frame 11 time 0.044 Reading frame 12 time 0.048 Reading frame 13 time 0.052 Reading frame 14 time 0.056 Reading frame 15 time 0.060 Reading frame 16 time 0.064 Reading frame 17 time 0.068 Reading frame 18 time 0.072 Reading frame 19 time 0.076 Reading frame 20 time 0.080 29: 29: Used 1 restart points spaced 200 ps over 0.1 ps 29: 29: This run will generate roughly 0 Mb of data 29: = 6.4731 Std. Dev. = 8.0969 Error = 3.6210 29: Fitting from 0.008 to 0.088 ps 29: 29: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s 29: [ OK ] MsdMolTest.diffMolNonMassWeighted (591 ms) 29: [ RUN ] MsdMolTest.diffMolSelected 29: 29: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]: 29: For a correct single-point energy evaluation with nsteps = 0, use 29: continuation = yes to avoid constraining the input coordinates. 29: 29: Setting the LD random seed to -36307497 29: Generated 330891 of the 330891 non-bonded parameter combinations 29: Generating 1-4 interactions: fudge = 0.5 29: Generated 330891 of the 330891 1-4 parameter combinations 29: Excluding 2 bonded neighbours molecule type 'SOL' 29: Number of degrees of freedom in T-Coupling group rest is 27.00 29: 29: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]: 29: NVE simulation with an initial temperature of zero: will use a Verlet 29: buffer of 10%. Check your energy drift! 29: 29: 29: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]: 29: You are using a plain Coulomb cut-off, which might produce artifacts. 29: You might want to consider using PME electrostatics. 29: 29: 29: 29: There were 3 notes 29: Calculating diffusion coefficients for molecules. 29: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 29: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 29: 29: Select a group to calculate mean squared displacement for: 29: Group 0 ( mol) has 9 elements 29: There is one group in the index 29: Split group of 9 atoms into 3 molecules 29: Reading frames from pdb file Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms 29: Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Reading frame 5 time 0.020 Reading frame 6 time 0.024 Reading frame 7 time 0.028 Reading frame 8 time 0.032 Reading frame 9 time 0.036 Reading frame 10 time 0.040 Reading frame 11 time 0.044 Reading frame 12 time 0.048 Reading frame 13 time 0.052 Reading frame 14 time 0.056 Reading frame 15 time 0.060 Reading frame 16 time 0.064 Reading frame 17 time 0.068 Reading frame 18 time 0.072 Reading frame 19 time 0.076 Reading frame 20 time 0.080 29: 29: Used 1 restart points spaced 200 ps over 0.1 ps 29: 29: This run will generate roughly 0 Mb of data 29: = 7.3593 Std. Dev. = 9.7910 Error = 5.6529 29: Fitting from 0.008 to 0.088 ps 29: 29: D[ mol] 7.8614 (+/- 1.5619) 1e-5 cm^2/s 29: [ OK ] MsdMolTest.diffMolSelected (755 ms) 29: [----------] 3 tests from MsdMolTest (2062 ms total) 29: 29: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj 29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 29: Group 0 ( System) has 6 elements 29: Group 1 ( Water) has 6 elements 29: Group 2 ( SOL) has 6 elements 29: Select a group: trr version: GMX_trn_file (single precision) 29: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 29: Selected 0: 'System' 29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (1 ms) 29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 29: Group 0 ( System) has 6 elements 29: Group 1 ( Water) has 6 elements 29: Group 2 ( SOL) has 6 elements 29: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 29: Selected 0: 'System' 29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (1 ms) 29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 29: Group 0 ( System) has 6 elements 29: Group 1 ( Water) has 6 elements 29: Group 2 ( SOL) has 6 elements 29: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 29: Selected 0: 'System' 29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (1 ms) 29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 29: Group 0 ( System) has 6 elements 29: Group 1 ( Water) has 6 elements 29: Group 2 ( SOL) has 6 elements 29: Select a group: Reading frames from gro file '', 6 atoms. 29: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 29: Selected 0: 'System' 29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (1 ms) 29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 29: Group 0 ( System) has 6 elements 29: Group 1 ( Water) has 6 elements 29: Group 2 ( SOL) has 6 elements 29: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 't= 0.00000', 6 atoms 29: Reading frame 1 time 0.000 Last frame 1 time 0.000 29: Selected 0: 'System' 29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (1 ms) 29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 29: Group 0 ( System) has 6 elements 29: Group 1 ( Water) has 6 elements 29: Group 2 ( SOL) has 6 elements 29: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 29: Selected 0: 'System' 29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (1 ms) 29: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj (6 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 27 tests from 5 test cases ran. (2086 ms total) 29: [ PASSED ] 27 tests. 29/54 Test #29: GmxAnaTest .......................... Passed 2.14 sec test 30 Start 30: GmxPreprocessTests 30: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/gmxpreprocess-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/GmxPreprocessTests.xml" 30: Test timeout computed to be: 30 30: [==========] Running 51 tests from 9 test cases. 30: [----------] Global test environment set-up. 30: [----------] 4 tests from GenconfTest 30: [ RUN ] GenconfTest.nbox_Works 30: [ OK ] GenconfTest.nbox_Works (2 ms) 30: [ RUN ] GenconfTest.nbox_norenumber_Works 30: [ OK ] GenconfTest.nbox_norenumber_Works (2 ms) 30: [ RUN ] GenconfTest.nbox_dist_Works 30: [ OK ] GenconfTest.nbox_dist_Works (2 ms) 30: [ RUN ] GenconfTest.nbox_rot_Works 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: center of geometry: 1.733667, 1.477000, 0.905167 30: [ OK ] GenconfTest.nbox_rot_Works (1 ms) 30: [----------] 4 tests from GenconfTest (8 ms total) 30: 30: [----------] 2 tests from GenionTest 30: [ RUN ] GenionTest.HighConcentrationIonPlacement 30: 30: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 30: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 30: buffer. The cluster pair list does have a buffering effect, but choosing 30: a larger rlist might be necessary for good energy conservation. 30: 30: 30: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: Setting the LD random seed to -369102874 30: Generated 331705 of the 331705 non-bonded parameter combinations 30: Generating 1-4 interactions: fudge = 0.5 30: Generated 331705 of the 331705 1-4 parameter combinations 30: Excluding 2 bonded neighbours molecule type 'SOL' 30: Excluding 3 bonded neighbours molecule type 'methane' 30: Number of degrees of freedom in T-Coupling group rest is 1308.00 30: 30: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 30: You are using a plain Coulomb cut-off, which might produce artifacts. 30: You might want to consider using PME electrostatics. 30: 30: 30: 30: There were 3 notes 30: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 30: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 30: Group 0 ( System) has 653 elements 30: Group 1 ( Water) has 648 elements 30: Group 2 ( SOL) has 648 elements 30: Group 3 ( non-Water) has 5 elements 30: Group 4 ( Other) has 5 elements 30: Group 5 ( METH) has 5 elements 30: Select a group: Number of (3-atomic) solvent molecules: 216 30: Using random seed 1997. 30: Replacing solvent molecule 56 (atom 168) with NA 30: Replacing solvent molecule 120 (atom 360) with NA 30: Replacing solvent molecule 182 (atom 546) with NA 30: Replacing solvent molecule 71 (atom 213) with NA 30: Replacing solvent molecule 189 (atom 567) with CL 30: Replacing solvent molecule 54 (atom 162) with CL 30: Replacing solvent molecule 155 (atom 465) with CL 30: Replacing solvent molecule 99 (atom 297) with CL 30: 30: Analysing residue names: 30: There are: 216 Water residues 30: There are: 1 Other residues 30: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 30: This run will generate roughly 0 Mb of data 30: Will try to add 4 NA ions and 4 CL ions. 30: Select a continuous group of solvent molecules 30: Selected 1: 'Water' 30: [ OK ] GenionTest.HighConcentrationIonPlacement (683 ms) 30: [ RUN ] GenionTest.NoIonPlacement 30: 30: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 30: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 30: buffer. The cluster pair list does have a buffering effect, but choosing 30: a larger rlist might be necessary for good energy conservation. 30: 30: 30: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: Setting the LD random seed to -78872842 30: Generated 331705 of the 331705 non-bonded parameter combinations 30: Generating 1-4 interactions: fudge = 0.5 30: Generated 331705 of the 331705 1-4 parameter combinations 30: Excluding 2 bonded neighbours molecule type 'SOL' 30: Excluding 3 bonded neighbours molecule type 'methane' 30: Number of degrees of freedom in T-Coupling group rest is 1308.00 30: 30: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 30: You are using a plain Coulomb cut-off, which might produce artifacts. 30: You might want to consider using PME electrostatics. 30: 30: 30: 30: There were 3 notes 30: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 30: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 30: No ions to add, will just copy input configuration. 30: Analysing residue names: 30: There are: 216 Water residues 30: There are: 1 Other residues 30: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 30: This run will generate roughly 0 Mb of data 30: [ OK ] GenionTest.NoIonPlacement (661 ms) 30: [----------] 2 tests from GenionTest (1344 ms total) 30: 30: [----------] 1 test from GenRestrTest 30: [ RUN ] GenRestrTest.SimpleRestraintsGenerated 30: 30: Reading structure file 30: Group 0 ( System) has 156 elements 30: Group 1 ( Protein) has 156 elements 30: Group 2 ( Protein-H) has 75 elements 30: Group 3 ( C-alpha) has 10 elements 30: Group 4 ( Backbone) has 30 elements 30: Group 5 ( MainChain) has 40 elements 30: Group 6 ( MainChain+Cb) has 49 elements 30: Group 7 ( MainChain+H) has 52 elements 30: Group 8 ( SideChain) has 104 elements 30: Group 9 ( SideChain-H) has 35 elements 30: Select a group: Select group to position restrain 30: Selected 3: 'C-alpha' 30: [ OK ] GenRestrTest.SimpleRestraintsGenerated (1 ms) 30: [----------] 1 test from GenRestrTest (1 ms total) 30: 30: [----------] 9 tests from PreprocessingAtomTypesTest 30: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate 30: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms) 30: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid 30: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms) 30: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks 30: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms) 30: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks 30: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms) 30: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry 30: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms) 30: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound 30: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms) 30: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound 30: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms) 30: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber 30: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms) 30: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber 30: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms) 30: [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total) 30: 30: [----------] 10 tests from PreprocessingBondAtomTypeTest 30: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate 30: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms) 30: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid 30: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms) 30: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks 30: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms) 30: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks 30: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms) 30: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry 30: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms) 30: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType 30: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms) 30: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound 30: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms) 30: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound 30: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms) 30: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber 30: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms) 30: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber 30: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms) 30: [----------] 10 tests from PreprocessingBondAtomTypeTest (1 ms total) 30: 30: [----------] 5 tests from InsertMoleculesTest 30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration 30: Reading solute configuration 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Using random seed 1997 30: Try 1 success (now 8 atoms)! 30: 30: Added 1 molecules (out of 1 requested) 30: Writing generated configuration to /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro 30: 30: Output configuration contains 8 atoms in 4 residues 30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (1 ms) 30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Using random seed 1997 30: Try 1 success (now 2 atoms)! 30: Try 2 success (now 4 atoms)! 30: Try 3 success (now 6 atoms)! 30: Try 4 success (now 8 atoms)! 30: Try 5 success (now 10 atoms)! 30: 30: Added 5 molecules (out of 5 requested) 30: Writing generated configuration to /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro 30: 30: Output configuration contains 10 atoms in 10 residues 30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (1 ms) 30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox 30: Reading solute configuration 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Using random seed 1997 30: Try 1 success (now 8 atoms)! 30: Try 2 success (now 10 atoms)! 30: 30: Added 2 molecules (out of 2 requested) 30: Writing generated configuration to /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro 30: 30: Output configuration contains 10 atoms in 4 residues 30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (1 ms) 30: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement 30: Reading solute configuration 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Using random seed 1997 30: Try 1 success (now 650 atoms)! 30: Try 2 success (now 652 atoms)! 30: Try 3 success (now 654 atoms)! 30: Try 4 success (now 656 atoms)! 30: 30: Added 4 molecules (out of 4 requested) 30: Replaced 8 residues (24 atoms) 30: Writing generated configuration to /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro 30: 30: Output configuration contains 632 atoms in 212 residues 30: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (33 ms) 30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Using random seed 1997 30: Read 4 positions from file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat 30: 30: Try 1 success (now 2 atoms)! 30: Try 2 success (now 4 atoms)! 30: Try 3 Try 4 Try 5 Try 6 Try 7 Try 8 Try 9 Try 10 Try 11 Try 12 skipped position (0.990, 2.010, 3.000) 30: Try 13 success (now 6 atoms)! 30: 30: Added 3 molecules (out of 4 requested) 30: Writing generated configuration to /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro 30: 30: Output configuration contains 6 atoms in 3 residues 30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (2 ms) 30: [----------] 5 tests from InsertMoleculesTest (38 ms total) 30: 30: [----------] 14 tests from GetIrTest 30: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines 30: Ignoring obsolete mdp entry 'title' 30: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' 30: 30: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (4 ms) 30: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals 30: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (8 ms) 30: [ RUN ] GetIrTest.AcceptsKeyWithoutValue 30: 30: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: [ OK ] GetIrTest.AcceptsKeyWithoutValue (4 ms) 30: [ RUN ] GetIrTest.RejectsValueWithoutKey 30: [ OK ] GetIrTest.RejectsValueWithoutKey (8 ms) 30: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue 30: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (7 ms) 30: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment 30: 30: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (4 ms) 30: [ RUN ] GetIrTest.AcceptsEmptyLines 30: 30: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: [ OK ] GetIrTest.AcceptsEmptyLines (4 ms) 30: [ RUN ] GetIrTest.AcceptsElectricField 30: 30: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: [ OK ] GetIrTest.AcceptsElectricField (4 ms) 30: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed 30: 30: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (5 ms) 30: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating 30: 30: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (4 ms) 30: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys 30: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (5 ms) 30: [ RUN ] GetIrTest.AcceptsImplicitSolventNo 30: 30: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: [ OK ] GetIrTest.AcceptsImplicitSolventNo (5 ms) 30: [ RUN ] GetIrTest.RejectsImplicitSolventYes 30: [ OK ] GetIrTest.RejectsImplicitSolventYes (36 ms) 30: [ RUN ] GetIrTest.AcceptsMimic 30: 30: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]: 30: For a correct single-point energy evaluation with nsteps = 0, use 30: continuation = yes to avoid constraining the input coordinates. 30: 30: [ OK ] GetIrTest.AcceptsMimic (5 ms) 30: [----------] 14 tests from GetIrTest (104 ms total) 30: 30: [----------] 5 tests from SolvateTest 30: [ RUN ] SolvateTest.cs_box_Works 30: Reading solvent configuration 30: 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Generating solvent configuration 30: Will generate new solvent configuration of 1x1x1 boxes 30: Solvent box contains 270 atoms in 90 residues 30: Removed 129 solvent atoms due to solvent-solvent overlap 30: Sorting configuration 30: Found 1 molecule type: 30: SOL ( 3 atoms): 47 residues 30: Generated solvent containing 141 atoms in 47 residues 30: Writing generated configuration to /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro 30: 30: Output configuration contains 141 atoms in 47 residues 30: Volume : 1.331 (nm^3) 30: Density : 1056.36 (g/l) 30: Number of solvent molecules: 47 30: 30: [ OK ] SolvateTest.cs_box_Works (13 ms) 30: [ RUN ] SolvateTest.cs_cp_Works 30: Reading solute configuration 30: Reading solvent configuration 30: 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Generating solvent configuration 30: Will generate new solvent configuration of 2x2x2 boxes 30: Solvent box contains 3660 atoms in 1220 residues 30: Removed 987 solvent atoms due to solvent-solvent overlap 30: Removed 15 solvent atoms due to solute-solvent overlap 30: Sorting configuration 30: Found 1 molecule type: 30: SOL ( 3 atoms): 886 residues 30: Generated solvent containing 2658 atoms in 886 residues 30: Writing generated configuration to /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro 30: 30: Output configuration contains 2664 atoms in 888 residues 30: Volume : 27.2709 (nm^3) 30: Density : 974.777 (g/l) 30: Number of solvent molecules: 886 30: 30: [ OK ] SolvateTest.cs_cp_Works (91 ms) 30: [ RUN ] SolvateTest.cs_cp_p_Works 30: Reading solute configuration 30: Reading solvent configuration 30: 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Generating solvent configuration 30: Will generate new solvent configuration of 2x2x2 boxes 30: Solvent box contains 3660 atoms in 1220 residues 30: Removed 987 solvent atoms due to solvent-solvent overlap 30: Removed 15 solvent atoms due to solute-solvent overlap 30: Sorting configuration 30: Found 1 molecule type: 30: SOL ( 3 atoms): 886 residues 30: Generated solvent containing 2658 atoms in 886 residues 30: Writing generated configuration to /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro 30: 30: Output configuration contains 2664 atoms in 888 residues 30: Volume : 27.2709 (nm^3) 30: Density : 974.777 (g/l) 30: Number of solvent molecules: 886 30: 30: Processing topology 30: Adding line for 886 solvent molecules with resname (SOL) to topology file (/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top) 30: [ OK ] SolvateTest.cs_cp_p_Works (95 ms) 30: [ RUN ] SolvateTest.shell_Works 30: Reading solute configuration 30: Reading solvent configuration 30: 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Generating solvent configuration 30: Will generate new solvent configuration of 2x2x2 boxes 30: Solvent box contains 3660 atoms in 1220 residues 30: Removed 987 solvent atoms due to solvent-solvent overlap 30: Removed 1902 solvent atoms more than 1.000000 nm from solute. 30: Removed 15 solvent atoms due to solute-solvent overlap 30: Sorting configuration 30: Found 1 molecule type: 30: SOL ( 3 atoms): 252 residues 30: Generated solvent containing 756 atoms in 252 residues 30: Writing generated configuration to /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro 30: 30: Output configuration contains 762 atoms in 254 residues 30: Volume : 27.2709 (nm^3) 30: Density : 279.3 (g/l) 30: Number of solvent molecules: 252 30: 30: [ OK ] SolvateTest.shell_Works (36 ms) 30: [ RUN ] SolvateTest.update_Topology_Works 30: Reading solute configuration 30: Reading solvent configuration 30: 30: Initialising inter-atomic distances... 30: 30: WARNING: Masses and atomic (Van der Waals) radii will be guessed 30: based on residue and atom names, since they could not be 30: definitively assigned from the information in your input 30: files. These guessed numbers might deviate from the mass 30: and radius of the atom type. Please check the output 30: files if necessary. 30: 30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 30: from the source below. This means the results may be different 30: compared to previous GROMACS versions. 30: 30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 30: A. Bondi 30: van der Waals Volumes and Radii 30: J. Phys. Chem. 68 (1964) pp. 441-451 30: -------- -------- --- Thank You --- -------- -------- 30: 30: Generating solvent configuration 30: Will generate new solvent configuration of 3x3x3 boxes 30: Solvent box contains 14952 atoms in 4984 residues 30: Removed 2787 solvent atoms due to solvent-solvent overlap 30: Removed 30 solvent atoms due to solute-solvent overlap 30: Sorting configuration 30: Found 2 different molecule types: 30: HOH ( 3 atoms): 1876 residues 30: SOL ( 3 atoms): 2169 residues 30: Generated solvent containing 0 atoms in 0 residues 30: Writing generated configuration to /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro 30: 30: Output configuration contains 12141 atoms in 4047 residues 30: Volume : 125 (nm^3) 30: Density : 968.963 (g/l) 30: Number of solvent molecules: 4045 30: 30: Processing topology 30: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 30: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 30: [ OK ] SolvateTest.update_Topology_Works (409 ms) 30: [----------] 5 tests from SolvateTest (644 ms total) 30: 30: [----------] 1 test from TopDirTests 30: [ RUN ] TopDirTests.NamesArrayHasCorrectSize 30: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms) 30: [----------] 1 test from TopDirTests (0 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 51 tests from 9 test cases ran. (2140 ms total) 30: [ PASSED ] 51 tests. 30/54 Test #30: GmxPreprocessTests .................. Passed 2.16 sec test 31 Start 31: Pdb2gmx1Test 31: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/pdb2gmx1-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/Pdb2gmx1Test.xml" 31: Test timeout computed to be: 30 31: [==========] Running 24 tests from 1 test case. 31: [----------] Global test environment set-up. 31: [----------] 24 tests from ForOplsaa/Pdb2gmxTest 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 25 donors and 23 acceptors were found. 31: There are 41 hydrogen bonds 31: Will use HISE for residue 8 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS3 HIS8 31: SG9 NE251 31: HIS8 NE251 1.055 31: MET12 SD83 0.763 0.990 31: Making bonds... 31: Number of bonds was 254, now 254 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 653 pairs 31: Before cleaning: 663 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 663 dihedrals, 51 impropers, 457 angles 31: 650 pairs, 254 bonds and 0 virtual sites 31: Total mass 1846.112 a.m.u. 31: Total charge 0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 128 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (128 atoms, 16 residues) 31: Identified residue ALA2 as a starting terminus. 31: Identified residue SER17 as a ending terminus. 31: Start terminus ALA-2: NH3+ 31: End terminus SER-17: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 252 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 31: The Oplsaa force field and the tip3p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0 (143 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 30 donors and 22 acceptors were found. 31: There are 36 hydrogen bonds 31: Will use HISE for residue 29 31: Will use HISE for residue 32 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS27 HIS29 31: SG90 NE2111 31: HIS29 NE2111 0.987 31: HIS32 NE2135 1.590 1.155 31: Making bonds... 31: Number of bonds was 290, now 290 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 748 pairs 31: Before cleaning: 778 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 778 dihedrals, 72 impropers, 516 angles 31: 736 pairs, 290 bonds and 0 virtual sites 31: Total mass 2088.357 a.m.u. 31: Total charge 1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 149 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (149 atoms, 16 residues) 31: Identified residue THR18 as a starting terminus. 31: Identified residue PHE33 as a ending terminus. 31: Start terminus THR-18: NH3+ 31: End terminus PHE-33: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 281 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 31: The Oplsaa force field and the tip3p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1 (141 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 22 acceptors were found. 31: There are 26 hydrogen bonds 31: Will use HISE for residue 45 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS45 31: NE295 31: MET46 SD102 1.078 31: Making bonds... 31: Number of bonds was 261, now 261 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 676 pairs 31: Before cleaning: 696 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 696 dihedrals, 56 impropers, 472 angles 31: 667 pairs, 261 bonds and 0 virtual sites 31: Total mass 1861.128 a.m.u. 31: Total charge -1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 132 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (132 atoms, 16 residues) 31: Identified residue ALA34 as a starting terminus. 31: Identified residue ALA49 as a ending terminus. 31: Start terminus ALA-34: NH3+ 31: End terminus ALA-49: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 255 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 31: The Oplsaa force field and the tip3p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2 (673 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 21 acceptors were found. 31: There are 30 hydrogen bonds 31: Will use HISE for residue 60 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS60 31: NE285 31: CYS62 SG98 0.803 31: Making bonds... 31: Number of bonds was 232, now 232 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 603 pairs 31: Before cleaning: 618 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 618 dihedrals, 48 impropers, 419 angles 31: 597 pairs, 232 bonds and 0 virtual sites 31: Total mass 1662.883 a.m.u. 31: Total charge 0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 117 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (117 atoms, 16 residues) 31: Identified residue LYS50 as a starting terminus. 31: Identified residue PRO65 as a ending terminus. 31: Start terminus LYS-50: NH3+ 31: End terminus PRO-65: PRO-COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 228 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 31: The Oplsaa force field and the tip3p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3 (1345 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 25 donors and 23 acceptors were found. 31: There are 41 hydrogen bonds 31: Will use HISE for residue 8 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS3 HIS8 31: SG9 NE251 31: HIS8 NE251 1.055 31: MET12 SD83 0.763 0.990 31: Making bonds... 31: Number of bonds was 254, now 254 31: Marked 124 virtual sites 31: Added 16 dummy masses 31: Added 26 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 653 pairs 31: Before cleaning: 663 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 663 dihedrals, 51 impropers, 457 angles 31: 650 pairs, 254 bonds and 130 virtual sites 31: Total mass 1846.112 a.m.u. 31: Total charge 0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 128 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (128 atoms, 16 residues) 31: Identified residue ALA2 as a starting terminus. 31: Identified residue SER17 as a ending terminus. 31: Start terminus ALA-2: NH3+ 31: End terminus SER-17: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 252 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 31: The Oplsaa force field and the tip3p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4 (239 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 30 donors and 22 acceptors were found. 31: There are 36 hydrogen bonds 31: Will use HISE for residue 29 31: Will use HISE for residue 32 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS27 HIS29 31: SG90 NE2111 31: HIS29 NE2111 0.987 31: HIS32 NE2135 1.590 1.155 31: Making bonds... 31: Number of bonds was 290, now 290 31: Marked 132 virtual sites 31: Added 10 dummy masses 31: Added 19 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 748 pairs 31: Before cleaning: 778 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 778 dihedrals, 72 impropers, 516 angles 31: 736 pairs, 290 bonds and 133 virtual sites 31: Total mass 2088.357 a.m.u. 31: Total charge 1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 149 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (149 atoms, 16 residues) 31: Identified residue THR18 as a starting terminus. 31: Identified residue PHE33 as a ending terminus. 31: Start terminus THR-18: NH3+ 31: End terminus PHE-33: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 281 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 31: The Oplsaa force field and the tip3p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5 (144 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 22 acceptors were found. 31: There are 26 hydrogen bonds 31: Will use HISE for residue 45 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS45 31: NE295 31: MET46 SD102 1.078 31: Making bonds... 31: Number of bonds was 261, now 261 31: Marked 123 virtual sites 31: Added 22 dummy masses 31: Added 35 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 676 pairs 31: Before cleaning: 696 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 696 dihedrals, 56 impropers, 472 angles 31: 667 pairs, 261 bonds and 132 virtual sites 31: Total mass 1861.128 a.m.u. 31: Total charge -1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 132 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (132 atoms, 16 residues) 31: Identified residue ALA34 as a starting terminus. 31: Identified residue ALA49 as a ending terminus. 31: Start terminus ALA-34: NH3+ 31: End terminus ALA-49: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 255 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 31: The Oplsaa force field and the tip3p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6 (133 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 21 acceptors were found. 31: There are 30 hydrogen bonds 31: Will use HISE for residue 60 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS60 31: NE285 31: CYS62 SG98 0.803 31: Making bonds... 31: Number of bonds was 232, now 232 31: Marked 111 virtual sites 31: Added 18 dummy masses 31: Added 31 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 603 pairs 31: Before cleaning: 618 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 618 dihedrals, 48 impropers, 419 angles 31: 597 pairs, 232 bonds and 116 virtual sites 31: Total mass 1662.883 a.m.u. 31: Total charge 0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 117 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (117 atoms, 16 residues) 31: Identified residue LYS50 as a starting terminus. 31: Identified residue PRO65 as a ending terminus. 31: Start terminus LYS-50: NH3+ 31: End terminus PRO-65: PRO-COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 228 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 31: The Oplsaa force field and the tip3p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7 (141 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 25 donors and 23 acceptors were found. 31: There are 41 hydrogen bonds 31: Will use HISE for residue 8 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS3 HIS8 31: SG9 NE251 31: HIS8 NE251 1.055 31: MET12 SD83 0.763 0.990 31: Making bonds... 31: Number of bonds was 254, now 254 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 653 pairs 31: Before cleaning: 663 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 663 dihedrals, 51 impropers, 457 angles 31: 650 pairs, 254 bonds and 0 virtual sites 31: Total mass 1846.112 a.m.u. 31: Total charge 0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 128 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (128 atoms, 16 residues) 31: Identified residue ALA2 as a starting terminus. 31: Identified residue SER17 as a ending terminus. 31: Start terminus ALA-2: NH3+ 31: End terminus SER-17: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 252 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 31: The Oplsaa force field and the tip4p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8 (93 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 30 donors and 22 acceptors were found. 31: There are 36 hydrogen bonds 31: Will use HISE for residue 29 31: Will use HISE for residue 32 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS27 HIS29 31: SG90 NE2111 31: HIS29 NE2111 0.987 31: HIS32 NE2135 1.590 1.155 31: Making bonds... 31: Number of bonds was 290, now 290 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 748 pairs 31: Before cleaning: 778 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 778 dihedrals, 72 impropers, 516 angles 31: 736 pairs, 290 bonds and 0 virtual sites 31: Total mass 2088.357 a.m.u. 31: Total charge 1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 149 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (149 atoms, 16 residues) 31: Identified residue THR18 as a starting terminus. 31: Identified residue PHE33 as a ending terminus. 31: Start terminus THR-18: NH3+ 31: End terminus PHE-33: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 281 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 31: The Oplsaa force field and the tip4p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9 (144 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 22 acceptors were found. 31: There are 26 hydrogen bonds 31: Will use HISE for residue 45 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS45 31: NE295 31: MET46 SD102 1.078 31: Making bonds... 31: Number of bonds was 261, now 261 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 676 pairs 31: Before cleaning: 696 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 696 dihedrals, 56 impropers, 472 angles 31: 667 pairs, 261 bonds and 0 virtual sites 31: Total mass 1861.128 a.m.u. 31: Total charge -1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 132 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (132 atoms, 16 residues) 31: Identified residue ALA34 as a starting terminus. 31: Identified residue ALA49 as a ending terminus. 31: Start terminus ALA-34: NH3+ 31: End terminus ALA-49: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 255 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 31: The Oplsaa force field and the tip4p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10 (171 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 21 acceptors were found. 31: There are 30 hydrogen bonds 31: Will use HISE for residue 60 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS60 31: NE285 31: CYS62 SG98 0.803 31: Making bonds... 31: Number of bonds was 232, now 232 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 603 pairs 31: Before cleaning: 618 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 618 dihedrals, 48 impropers, 419 angles 31: 597 pairs, 232 bonds and 0 virtual sites 31: Total mass 1662.883 a.m.u. 31: Total charge 0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 117 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (117 atoms, 16 residues) 31: Identified residue LYS50 as a starting terminus. 31: Identified residue PRO65 as a ending terminus. 31: Start terminus LYS-50: NH3+ 31: End terminus PRO-65: PRO-COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 228 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 31: The Oplsaa force field and the tip4p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11 (105 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 25 donors and 23 acceptors were found. 31: There are 41 hydrogen bonds 31: Will use HISE for residue 8 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS3 HIS8 31: SG9 NE251 31: HIS8 NE251 1.055 31: MET12 SD83 0.763 0.990 31: Making bonds... 31: Number of bonds was 254, now 254 31: Marked 124 virtual sites 31: Added 16 dummy masses 31: Added 26 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 653 pairs 31: Before cleaning: 663 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 663 dihedrals, 51 impropers, 457 angles 31: 650 pairs, 254 bonds and 130 virtual sites 31: Total mass 1846.112 a.m.u. 31: Total charge 0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 128 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (128 atoms, 16 residues) 31: Identified residue ALA2 as a starting terminus. 31: Identified residue SER17 as a ending terminus. 31: Start terminus ALA-2: NH3+ 31: End terminus SER-17: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 252 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 31: The Oplsaa force field and the tip4p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12 (121 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 30 donors and 22 acceptors were found. 31: There are 36 hydrogen bonds 31: Will use HISE for residue 29 31: Will use HISE for residue 32 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS27 HIS29 31: SG90 NE2111 31: HIS29 NE2111 0.987 31: HIS32 NE2135 1.590 1.155 31: Making bonds... 31: Number of bonds was 290, now 290 31: Marked 132 virtual sites 31: Added 10 dummy masses 31: Added 19 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 748 pairs 31: Before cleaning: 778 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 778 dihedrals, 72 impropers, 516 angles 31: 736 pairs, 290 bonds and 133 virtual sites 31: Total mass 2088.357 a.m.u. 31: Total charge 1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 149 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (149 atoms, 16 residues) 31: Identified residue THR18 as a starting terminus. 31: Identified residue PHE33 as a ending terminus. 31: Start terminus THR-18: NH3+ 31: End terminus PHE-33: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 281 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 31: The Oplsaa force field and the tip4p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13 (97 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 22 acceptors were found. 31: There are 26 hydrogen bonds 31: Will use HISE for residue 45 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS45 31: NE295 31: MET46 SD102 1.078 31: Making bonds... 31: Number of bonds was 261, now 261 31: Marked 123 virtual sites 31: Added 22 dummy masses 31: Added 35 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 676 pairs 31: Before cleaning: 696 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 696 dihedrals, 56 impropers, 472 angles 31: 667 pairs, 261 bonds and 132 virtual sites 31: Total mass 1861.128 a.m.u. 31: Total charge -1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 132 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (132 atoms, 16 residues) 31: Identified residue ALA34 as a starting terminus. 31: Identified residue ALA49 as a ending terminus. 31: Start terminus ALA-34: NH3+ 31: End terminus ALA-49: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 255 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 31: The Oplsaa force field and the tip4p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14 (181 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 21 acceptors were found. 31: There are 30 hydrogen bonds 31: Will use HISE for residue 60 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS60 31: NE285 31: CYS62 SG98 0.803 31: Making bonds... 31: Number of bonds was 232, now 232 31: Marked 111 virtual sites 31: Added 18 dummy masses 31: Added 31 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 603 pairs 31: Before cleaning: 618 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 618 dihedrals, 48 impropers, 419 angles 31: 597 pairs, 232 bonds and 116 virtual sites 31: Total mass 1662.883 a.m.u. 31: Total charge 0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 117 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (117 atoms, 16 residues) 31: Identified residue LYS50 as a starting terminus. 31: Identified residue PRO65 as a ending terminus. 31: Start terminus LYS-50: NH3+ 31: End terminus PRO-65: PRO-COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 228 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 31: The Oplsaa force field and the tip4p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15 (115 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 25 donors and 23 acceptors were found. 31: There are 41 hydrogen bonds 31: Will use HISE for residue 8 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS3 HIS8 31: SG9 NE251 31: HIS8 NE251 1.055 31: MET12 SD83 0.763 0.990 31: Making bonds... 31: Number of bonds was 254, now 254 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 653 pairs 31: Before cleaning: 663 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 663 dihedrals, 51 impropers, 457 angles 31: 650 pairs, 254 bonds and 0 virtual sites 31: Total mass 1846.112 a.m.u. 31: Total charge 0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 128 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (128 atoms, 16 residues) 31: Identified residue ALA2 as a starting terminus. 31: Identified residue SER17 as a ending terminus. 31: Start terminus ALA-2: NH3+ 31: End terminus SER-17: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 252 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 31: The Oplsaa force field and the tip5p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16 (155 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 30 donors and 22 acceptors were found. 31: There are 36 hydrogen bonds 31: Will use HISE for residue 29 31: Will use HISE for residue 32 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS27 HIS29 31: SG90 NE2111 31: HIS29 NE2111 0.987 31: HIS32 NE2135 1.590 1.155 31: Making bonds... 31: Number of bonds was 290, now 290 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 748 pairs 31: Before cleaning: 778 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 778 dihedrals, 72 impropers, 516 angles 31: 736 pairs, 290 bonds and 0 virtual sites 31: Total mass 2088.357 a.m.u. 31: Total charge 1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 149 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (149 atoms, 16 residues) 31: Identified residue THR18 as a starting terminus. 31: Identified residue PHE33 as a ending terminus. 31: Start terminus THR-18: NH3+ 31: End terminus PHE-33: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 281 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 31: The Oplsaa force field and the tip5p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17 (132 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 22 acceptors were found. 31: There are 26 hydrogen bonds 31: Will use HISE for residue 45 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS45 31: NE295 31: MET46 SD102 1.078 31: Making bonds... 31: Number of bonds was 261, now 261 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 676 pairs 31: Before cleaning: 696 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 696 dihedrals, 56 impropers, 472 angles 31: 667 pairs, 261 bonds and 0 virtual sites 31: Total mass 1861.128 a.m.u. 31: Total charge -1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 132 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (132 atoms, 16 residues) 31: Identified residue ALA34 as a starting terminus. 31: Identified residue ALA49 as a ending terminus. 31: Start terminus ALA-34: NH3+ 31: End terminus ALA-49: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 255 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 31: The Oplsaa force field and the tip5p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18 (115 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 21 acceptors were found. 31: There are 30 hydrogen bonds 31: Will use HISE for residue 60 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS60 31: NE285 31: CYS62 SG98 0.803 31: Making bonds... 31: Number of bonds was 232, now 232 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 603 pairs 31: Before cleaning: 618 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 618 dihedrals, 48 impropers, 419 angles 31: 597 pairs, 232 bonds and 0 virtual sites 31: Total mass 1662.883 a.m.u. 31: Total charge 0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 117 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (117 atoms, 16 residues) 31: Identified residue LYS50 as a starting terminus. 31: Identified residue PRO65 as a ending terminus. 31: Start terminus LYS-50: NH3+ 31: End terminus PRO-65: PRO-COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 228 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 31: The Oplsaa force field and the tip5p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19 (114 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 25 donors and 23 acceptors were found. 31: There are 41 hydrogen bonds 31: Will use HISE for residue 8 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS3 HIS8 31: SG9 NE251 31: HIS8 NE251 1.055 31: MET12 SD83 0.763 0.990 31: Making bonds... 31: Number of bonds was 254, now 254 31: Marked 124 virtual sites 31: Added 16 dummy masses 31: Added 26 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 653 pairs 31: Before cleaning: 663 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 663 dihedrals, 51 impropers, 457 angles 31: 650 pairs, 254 bonds and 130 virtual sites 31: Total mass 1846.112 a.m.u. 31: Total charge 0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 128 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (128 atoms, 16 residues) 31: Identified residue ALA2 as a starting terminus. 31: Identified residue SER17 as a ending terminus. 31: Start terminus ALA-2: NH3+ 31: End terminus SER-17: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 252 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 31: The Oplsaa force field and the tip5p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20 (242 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 30 donors and 22 acceptors were found. 31: There are 36 hydrogen bonds 31: Will use HISE for residue 29 31: Will use HISE for residue 32 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: CYS27 HIS29 31: SG90 NE2111 31: HIS29 NE2111 0.987 31: HIS32 NE2135 1.590 1.155 31: Making bonds... 31: Number of bonds was 290, now 290 31: Marked 132 virtual sites 31: Added 10 dummy masses 31: Added 19 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 748 pairs 31: Before cleaning: 778 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 778 dihedrals, 72 impropers, 516 angles 31: 736 pairs, 290 bonds and 133 virtual sites 31: Total mass 2088.357 a.m.u. 31: Total charge 1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 149 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (149 atoms, 16 residues) 31: Identified residue THR18 as a starting terminus. 31: Identified residue PHE33 as a ending terminus. 31: Start terminus THR-18: NH3+ 31: End terminus PHE-33: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 281 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 31: The Oplsaa force field and the tip5p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21 (150 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 22 acceptors were found. 31: There are 26 hydrogen bonds 31: Will use HISE for residue 45 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS45 31: NE295 31: MET46 SD102 1.078 31: Making bonds... 31: Number of bonds was 261, now 261 31: Marked 123 virtual sites 31: Added 22 dummy masses 31: Added 35 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 676 pairs 31: Before cleaning: 696 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 696 dihedrals, 56 impropers, 472 angles 31: 667 pairs, 261 bonds and 132 virtual sites 31: Total mass 1861.128 a.m.u. 31: Total charge -1.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 132 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (132 atoms, 16 residues) 31: Identified residue ALA34 as a starting terminus. 31: Identified residue ALA49 as a ending terminus. 31: Start terminus ALA-34: NH3+ 31: End terminus ALA-49: COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 255 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 31: The Oplsaa force field and the tip5p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22 (148 ms) 31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.r2b 31: All occupancies are one 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/atomtypes.atp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.rtp 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.hdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.n.tdb 31: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/oplsaa.ff/aminoacids.c.tdb 31: Analysing hydrogen-bonding network for automated assignment of histidine 31: protonation. 22 donors and 21 acceptors were found. 31: There are 30 hydrogen bonds 31: Will use HISE for residue 60 31: 8 out of 8 lines of specbond.dat converted successfully 31: Special Atom Distance matrix: 31: HIS60 31: NE285 31: CYS62 SG98 0.803 31: Making bonds... 31: Number of bonds was 232, now 232 31: Marked 111 virtual sites 31: Added 18 dummy masses 31: Added 31 new constraints 31: Generating angles, dihedrals and pairs... 31: Before cleaning: 603 pairs 31: Before cleaning: 618 dihedrals 31: Keeping all generated dihedrals 31: Making cmap torsions... 31: There are 618 dihedrals, 48 impropers, 419 angles 31: 597 pairs, 232 bonds and 116 virtual sites 31: Total mass 1662.883 a.m.u. 31: Total charge 0.000 e 31: Writing topology 31: 31: Writing coordinate file... 31: 31: Using the Oplsaa force field in directory oplsaa.ff 31: 31: going to rename oplsaa.ff/aminoacids.r2b 31: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 31: Analyzing pdb file 31: Splitting chemical chains based on TER records or chain id changing. 31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 31: 31: chain #res #atoms 31: 1 ' ' 16 117 31: 31: Reading residue database... (Oplsaa) 31: Processing chain 1 (117 atoms, 16 residues) 31: Identified residue LYS50 as a starting terminus. 31: Identified residue PRO65 as a ending terminus. 31: Start terminus LYS-50: NH3+ 31: End terminus PRO-65: PRO-COO- 31: Checking for duplicate atoms.... 31: Generating any missing hydrogen atoms and/or adding termini. 31: Now there are 16 residues with 228 atoms 31: --------- PLEASE NOTE ------------ 31: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 31: The Oplsaa force field and the tip5p water model are used. 31: --------- ETON ESAELP ------------ 31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23 (143 ms) 31: [----------] 24 tests from ForOplsaa/Pdb2gmxTest (5185 ms total) 31: 31: [----------] Global test environment tear-down 31: [==========] 24 tests from 1 test case ran. (5185 ms total) 31: [ PASSED ] 24 tests. 31/54 Test #31: Pdb2gmx1Test ........................ Passed 5.20 sec test 32 Start 32: Pdb2gmx2Test 32: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/pdb2gmx2-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/Pdb2gmx2Test.xml" 32: Test timeout computed to be: 30 32: [==========] Running 32 tests from 2 test cases. 32: [----------] Global test environment set-up. 32: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 25 donors and 23 acceptors were found. 32: There are 41 hydrogen bonds 32: Will use HISE for residue 8 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS3 HIS8 32: SG9 NE251 32: HIS8 NE251 1.055 32: MET12 SD83 0.763 0.990 32: Making bonds... 32: Number of bonds was 172, now 167 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 267 pairs 32: Before cleaning: 305 dihedrals 32: Making cmap torsions... 32: There are 90 dihedrals, 77 impropers, 241 angles 32: 267 pairs, 167 bonds and 0 virtual sites 32: Total mass 1846.116 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 128 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (128 atoms, 16 residues) 32: Identified residue ALA2 as a starting terminus. 32: Identified residue SER17 as a ending terminus. 32: Start terminus ALA-2: NH3+ 32: End terminus SER-17: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 165 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 32: The Gromos43a1 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0 (116 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 30 donors and 22 acceptors were found. 32: There are 36 hydrogen bonds 32: Will use HISE for residue 29 32: Will use HISE for residue 32 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS27 HIS29 32: SG90 NE2111 32: HIS29 NE2111 0.987 32: HIS32 NE2135 1.590 1.155 32: Making bonds... 32: Number of bonds was 216, now 211 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 273 pairs 32: Before cleaning: 429 dihedrals 32: Making cmap torsions... 32: There are 93 dihedrals, 134 impropers, 316 angles 32: 273 pairs, 211 bonds and 0 virtual sites 32: Total mass 2088.361 a.m.u. 32: Total charge 1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 149 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (149 atoms, 16 residues) 32: Identified residue THR18 as a starting terminus. 32: Identified residue PHE33 as a ending terminus. 32: Start terminus THR-18: NH3+ 32: End terminus PHE-33: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 202 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 32: The Gromos43a1 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1 (107 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 22 acceptors were found. 32: There are 26 hydrogen bonds 32: Will use HISE for residue 45 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS45 32: NE295 32: MET46 SD102 1.078 32: Making bonds... 32: Number of bonds was 179, now 174 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 242 pairs 32: Before cleaning: 349 dihedrals 32: Making cmap torsions... 32: There are 81 dihedrals, 102 impropers, 260 angles 32: 242 pairs, 174 bonds and 0 virtual sites 32: Total mass 1861.132 a.m.u. 32: Total charge -1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 132 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (132 atoms, 16 residues) 32: Identified residue ALA34 as a starting terminus. 32: Identified residue ALA49 as a ending terminus. 32: Start terminus ALA-34: NH3+ 32: End terminus ALA-49: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 168 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 32: The Gromos43a1 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2 (86 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 21 acceptors were found. 32: There are 30 hydrogen bonds 32: Will use HISE for residue 60 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS60 32: NE285 32: CYS62 SG98 0.803 32: Making bonds... 32: Number of bonds was 159, now 154 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 232 pairs 32: Before cleaning: 299 dihedrals 32: Making cmap torsions... 32: There are 78 dihedrals, 80 impropers, 227 angles 32: 232 pairs, 154 bonds and 0 virtual sites 32: Total mass 1662.887 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 117 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (117 atoms, 16 residues) 32: Identified residue LYS50 as a starting terminus. 32: Identified residue PRO65 as a ending terminus. 32: Start terminus LYS-50: NH3+ 32: End terminus PRO-65: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 150 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 32: The Gromos43a1 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3 (115 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 25 donors and 23 acceptors were found. 32: There are 41 hydrogen bonds 32: Will use HISE for residue 8 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS3 HIS8 32: SG9 NE251 32: HIS8 NE251 1.055 32: MET12 SD83 0.763 0.990 32: Making bonds... 32: Number of bonds was 172, now 167 32: Marked 37 virtual sites 32: Added 4 dummy masses 32: Added 8 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 267 pairs 32: Before cleaning: 305 dihedrals 32: Making cmap torsions... 32: There are 90 dihedrals, 77 impropers, 241 angles 32: 267 pairs, 167 bonds and 37 virtual sites 32: Total mass 1846.116 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 128 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (128 atoms, 16 residues) 32: Identified residue ALA2 as a starting terminus. 32: Identified residue SER17 as a ending terminus. 32: Start terminus ALA-2: NH3+ 32: End terminus SER-17: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 165 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 32: The Gromos43a1 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4 (89 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 30 donors and 22 acceptors were found. 32: There are 36 hydrogen bonds 32: Will use HISE for residue 29 32: Will use HISE for residue 32 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS27 HIS29 32: SG90 NE2111 32: HIS29 NE2111 0.987 32: HIS32 NE2135 1.590 1.155 32: Making bonds... 32: Number of bonds was 216, now 211 32: Marked 53 virtual sites 32: Added 4 dummy masses 32: Added 10 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 273 pairs 32: Before cleaning: 429 dihedrals 32: Making cmap torsions... 32: There are 93 dihedrals, 134 impropers, 316 angles 32: 273 pairs, 211 bonds and 51 virtual sites 32: Total mass 2088.361 a.m.u. 32: Total charge 1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 149 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (149 atoms, 16 residues) 32: Identified residue THR18 as a starting terminus. 32: Identified residue PHE33 as a ending terminus. 32: Start terminus THR-18: NH3+ 32: End terminus PHE-33: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 202 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 32: The Gromos43a1 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5 (97 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 22 acceptors were found. 32: There are 26 hydrogen bonds 32: Will use HISE for residue 45 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS45 32: NE295 32: MET46 SD102 1.078 32: Making bonds... 32: Number of bonds was 179, now 174 32: Marked 36 virtual sites 32: Added 4 dummy masses 32: Added 8 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 242 pairs 32: Before cleaning: 349 dihedrals 32: Making cmap torsions... 32: There are 81 dihedrals, 102 impropers, 260 angles 32: 242 pairs, 174 bonds and 36 virtual sites 32: Total mass 1861.132 a.m.u. 32: Total charge -1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 132 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (132 atoms, 16 residues) 32: Identified residue ALA34 as a starting terminus. 32: Identified residue ALA49 as a ending terminus. 32: Start terminus ALA-34: NH3+ 32: End terminus ALA-49: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 168 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 32: The Gromos43a1 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6 (52 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 21 acceptors were found. 32: There are 30 hydrogen bonds 32: Will use HISE for residue 60 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS60 32: NE285 32: CYS62 SG98 0.803 32: Making bonds... 32: Number of bonds was 159, now 154 32: Marked 33 virtual sites 32: Added 4 dummy masses 32: Added 10 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 232 pairs 32: Before cleaning: 299 dihedrals 32: Making cmap torsions... 32: There are 78 dihedrals, 80 impropers, 227 angles 32: 232 pairs, 154 bonds and 31 virtual sites 32: Total mass 1662.887 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 117 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (117 atoms, 16 residues) 32: Identified residue LYS50 as a starting terminus. 32: Identified residue PRO65 as a ending terminus. 32: Start terminus LYS-50: NH3+ 32: End terminus PRO-65: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 150 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 32: The Gromos43a1 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7 (78 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 25 donors and 23 acceptors were found. 32: There are 41 hydrogen bonds 32: Will use HISE for residue 8 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS3 HIS8 32: SG9 NE251 32: HIS8 NE251 1.055 32: MET12 SD83 0.763 0.990 32: Making bonds... 32: Number of bonds was 172, now 167 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 267 pairs 32: Before cleaning: 305 dihedrals 32: Making cmap torsions... 32: There are 90 dihedrals, 77 impropers, 241 angles 32: 267 pairs, 167 bonds and 0 virtual sites 32: Total mass 1846.116 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 128 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (128 atoms, 16 residues) 32: Identified residue ALA2 as a starting terminus. 32: Identified residue SER17 as a ending terminus. 32: Start terminus ALA-2: NH3+ 32: End terminus SER-17: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 165 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 32: The Gromos43a1 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8 (97 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 30 donors and 22 acceptors were found. 32: There are 36 hydrogen bonds 32: Will use HISE for residue 29 32: Will use HISE for residue 32 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS27 HIS29 32: SG90 NE2111 32: HIS29 NE2111 0.987 32: HIS32 NE2135 1.590 1.155 32: Making bonds... 32: Number of bonds was 216, now 211 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 273 pairs 32: Before cleaning: 429 dihedrals 32: Making cmap torsions... 32: There are 93 dihedrals, 134 impropers, 316 angles 32: 273 pairs, 211 bonds and 0 virtual sites 32: Total mass 2088.361 a.m.u. 32: Total charge 1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 149 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (149 atoms, 16 residues) 32: Identified residue THR18 as a starting terminus. 32: Identified residue PHE33 as a ending terminus. 32: Start terminus THR-18: NH3+ 32: End terminus PHE-33: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 202 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 32: The Gromos43a1 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9 (104 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 22 acceptors were found. 32: There are 26 hydrogen bonds 32: Will use HISE for residue 45 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS45 32: NE295 32: MET46 SD102 1.078 32: Making bonds... 32: Number of bonds was 179, now 174 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 242 pairs 32: Before cleaning: 349 dihedrals 32: Making cmap torsions... 32: There are 81 dihedrals, 102 impropers, 260 angles 32: 242 pairs, 174 bonds and 0 virtual sites 32: Total mass 1861.132 a.m.u. 32: Total charge -1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 132 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (132 atoms, 16 residues) 32: Identified residue ALA34 as a starting terminus. 32: Identified residue ALA49 as a ending terminus. 32: Start terminus ALA-34: NH3+ 32: End terminus ALA-49: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 168 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 32: The Gromos43a1 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10 (71 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 21 acceptors were found. 32: There are 30 hydrogen bonds 32: Will use HISE for residue 60 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS60 32: NE285 32: CYS62 SG98 0.803 32: Making bonds... 32: Number of bonds was 159, now 154 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 232 pairs 32: Before cleaning: 299 dihedrals 32: Making cmap torsions... 32: There are 78 dihedrals, 80 impropers, 227 angles 32: 232 pairs, 154 bonds and 0 virtual sites 32: Total mass 1662.887 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 117 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (117 atoms, 16 residues) 32: Identified residue LYS50 as a starting terminus. 32: Identified residue PRO65 as a ending terminus. 32: Start terminus LYS-50: NH3+ 32: End terminus PRO-65: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 150 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 32: The Gromos43a1 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11 (101 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 25 donors and 23 acceptors were found. 32: There are 41 hydrogen bonds 32: Will use HISE for residue 8 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS3 HIS8 32: SG9 NE251 32: HIS8 NE251 1.055 32: MET12 SD83 0.763 0.990 32: Making bonds... 32: Number of bonds was 172, now 167 32: Marked 37 virtual sites 32: Added 4 dummy masses 32: Added 8 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 267 pairs 32: Before cleaning: 305 dihedrals 32: Making cmap torsions... 32: There are 90 dihedrals, 77 impropers, 241 angles 32: 267 pairs, 167 bonds and 37 virtual sites 32: Total mass 1846.116 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 128 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (128 atoms, 16 residues) 32: Identified residue ALA2 as a starting terminus. 32: Identified residue SER17 as a ending terminus. 32: Start terminus ALA-2: NH3+ 32: End terminus SER-17: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 165 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 32: The Gromos43a1 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12 (57 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 30 donors and 22 acceptors were found. 32: There are 36 hydrogen bonds 32: Will use HISE for residue 29 32: Will use HISE for residue 32 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS27 HIS29 32: SG90 NE2111 32: HIS29 NE2111 0.987 32: HIS32 NE2135 1.590 1.155 32: Making bonds... 32: Number of bonds was 216, now 211 32: Marked 53 virtual sites 32: Added 4 dummy masses 32: Added 10 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 273 pairs 32: Before cleaning: 429 dihedrals 32: Making cmap torsions... 32: There are 93 dihedrals, 134 impropers, 316 angles 32: 273 pairs, 211 bonds and 51 virtual sites 32: Total mass 2088.361 a.m.u. 32: Total charge 1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 149 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (149 atoms, 16 residues) 32: Identified residue THR18 as a starting terminus. 32: Identified residue PHE33 as a ending terminus. 32: Start terminus THR-18: NH3+ 32: End terminus PHE-33: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 202 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 32: The Gromos43a1 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13 (95 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 22 acceptors were found. 32: There are 26 hydrogen bonds 32: Will use HISE for residue 45 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS45 32: NE295 32: MET46 SD102 1.078 32: Making bonds... 32: Number of bonds was 179, now 174 32: Marked 36 virtual sites 32: Added 4 dummy masses 32: Added 8 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 242 pairs 32: Before cleaning: 349 dihedrals 32: Making cmap torsions... 32: There are 81 dihedrals, 102 impropers, 260 angles 32: 242 pairs, 174 bonds and 36 virtual sites 32: Total mass 1861.132 a.m.u. 32: Total charge -1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 132 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (132 atoms, 16 residues) 32: Identified residue ALA34 as a starting terminus. 32: Identified residue ALA49 as a ending terminus. 32: Start terminus ALA-34: NH3+ 32: End terminus ALA-49: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 168 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 32: The Gromos43a1 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14 (92 ms) 32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.rtp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos43a1.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 21 acceptors were found. 32: There are 30 hydrogen bonds 32: Will use HISE for residue 60 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS60 32: NE285 32: CYS62 SG98 0.803 32: Making bonds... 32: Number of bonds was 159, now 154 32: Marked 33 virtual sites 32: Added 4 dummy masses 32: Added 10 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 232 pairs 32: Before cleaning: 299 dihedrals 32: Making cmap torsions... 32: There are 78 dihedrals, 80 impropers, 227 angles 32: 232 pairs, 154 bonds and 31 virtual sites 32: Total mass 1662.887 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos43a1 force field in directory gromos43a1.ff 32: 32: going to rename gromos43a1.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 117 32: 32: Reading residue database... (Gromos43a1) 32: Processing chain 1 (117 atoms, 16 residues) 32: Identified residue LYS50 as a starting terminus. 32: Identified residue PRO65 as a ending terminus. 32: Start terminus LYS-50: NH3+ 32: End terminus PRO-65: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 150 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 32: The Gromos43a1 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15 (83 ms) 32: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest (1441 ms total) 32: 32: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 25 donors and 23 acceptors were found. 32: There are 41 hydrogen bonds 32: Will use HISE for residue 8 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS3 HIS8 32: SG9 NE251 32: HIS8 NE251 1.055 32: MET12 SD83 0.763 0.990 32: Making bonds... 32: Number of bonds was 174, now 169 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 267 pairs 32: Before cleaning: 312 dihedrals 32: Making cmap torsions... 32: There are 90 dihedrals, 79 impropers, 245 angles 32: 267 pairs, 169 bonds and 0 virtual sites 32: Total mass 1846.116 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 128 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (128 atoms, 16 residues) 32: Identified residue ALA2 as a starting terminus. 32: Identified residue SER17 as a ending terminus. 32: Start terminus ALA-2: NH3+ 32: End terminus SER-17: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 167 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 32: The Gromos53a6 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0 (79 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 30 donors and 22 acceptors were found. 32: There are 36 hydrogen bonds 32: Will use HISE for residue 29 32: Will use HISE for residue 32 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS27 HIS29 32: SG90 NE2111 32: HIS29 NE2111 0.987 32: HIS32 NE2135 1.590 1.155 32: Making bonds... 32: Number of bonds was 220, now 215 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 273 pairs 32: Before cleaning: 443 dihedrals 32: Making cmap torsions... 32: There are 93 dihedrals, 138 impropers, 324 angles 32: 273 pairs, 215 bonds and 0 virtual sites 32: Total mass 2088.361 a.m.u. 32: Total charge 1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 149 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (149 atoms, 16 residues) 32: Identified residue THR18 as a starting terminus. 32: Identified residue PHE33 as a ending terminus. 32: Start terminus THR-18: NH3+ 32: End terminus PHE-33: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 206 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 32: The Gromos53a6 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1 (93 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 22 acceptors were found. 32: There are 26 hydrogen bonds 32: Will use HISE for residue 45 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS45 32: NE295 32: MET46 SD102 1.078 32: Making bonds... 32: Number of bonds was 181, now 176 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 242 pairs 32: Before cleaning: 356 dihedrals 32: Making cmap torsions... 32: There are 81 dihedrals, 104 impropers, 264 angles 32: 242 pairs, 176 bonds and 0 virtual sites 32: Total mass 1861.132 a.m.u. 32: Total charge -1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 132 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (132 atoms, 16 residues) 32: Identified residue ALA34 as a starting terminus. 32: Identified residue ALA49 as a ending terminus. 32: Start terminus ALA-34: NH3+ 32: End terminus ALA-49: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 170 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 32: The Gromos53a6 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2 (56 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 21 acceptors were found. 32: There are 30 hydrogen bonds 32: Will use HISE for residue 60 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS60 32: NE285 32: CYS62 SG98 0.803 32: Making bonds... 32: Number of bonds was 161, now 156 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 232 pairs 32: Before cleaning: 306 dihedrals 32: Making cmap torsions... 32: There are 78 dihedrals, 82 impropers, 231 angles 32: 232 pairs, 156 bonds and 0 virtual sites 32: Total mass 1662.887 a.m.u. 32: Total charge -0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 117 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (117 atoms, 16 residues) 32: Identified residue LYS50 as a starting terminus. 32: Identified residue PRO65 as a ending terminus. 32: Start terminus LYS-50: NH3+ 32: End terminus PRO-65: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 152 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 32: The Gromos53a6 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3 (93 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 25 donors and 23 acceptors were found. 32: There are 41 hydrogen bonds 32: Will use HISE for residue 8 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS3 HIS8 32: SG9 NE251 32: HIS8 NE251 1.055 32: MET12 SD83 0.763 0.990 32: Making bonds... 32: Number of bonds was 174, now 169 32: Marked 39 virtual sites 32: Added 4 dummy masses 32: Added 8 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 267 pairs 32: Before cleaning: 312 dihedrals 32: Making cmap torsions... 32: There are 90 dihedrals, 79 impropers, 245 angles 32: 267 pairs, 169 bonds and 39 virtual sites 32: Total mass 1846.116 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 128 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (128 atoms, 16 residues) 32: Identified residue ALA2 as a starting terminus. 32: Identified residue SER17 as a ending terminus. 32: Start terminus ALA-2: NH3+ 32: End terminus SER-17: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 167 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 32: The Gromos53a6 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4 (97 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 30 donors and 22 acceptors were found. 32: There are 36 hydrogen bonds 32: Will use HISE for residue 29 32: Will use HISE for residue 32 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS27 HIS29 32: SG90 NE2111 32: HIS29 NE2111 0.987 32: HIS32 NE2135 1.590 1.155 32: Making bonds... 32: Number of bonds was 220, now 215 32: Marked 57 virtual sites 32: Added 4 dummy masses 32: Added 10 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 273 pairs 32: Before cleaning: 443 dihedrals 32: Making cmap torsions... 32: There are 93 dihedrals, 138 impropers, 324 angles 32: 273 pairs, 215 bonds and 55 virtual sites 32: Total mass 2088.361 a.m.u. 32: Total charge 1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 149 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (149 atoms, 16 residues) 32: Identified residue THR18 as a starting terminus. 32: Identified residue PHE33 as a ending terminus. 32: Start terminus THR-18: NH3+ 32: End terminus PHE-33: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 206 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 32: The Gromos53a6 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5 (145 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 22 acceptors were found. 32: There are 26 hydrogen bonds 32: Will use HISE for residue 45 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS45 32: NE295 32: MET46 SD102 1.078 32: Making bonds... 32: Number of bonds was 181, now 176 32: Marked 38 virtual sites 32: Added 4 dummy masses 32: Added 8 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 242 pairs 32: Before cleaning: 356 dihedrals 32: Making cmap torsions... 32: There are 81 dihedrals, 104 impropers, 264 angles 32: 242 pairs, 176 bonds and 38 virtual sites 32: Total mass 1861.132 a.m.u. 32: Total charge -1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 132 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (132 atoms, 16 residues) 32: Identified residue ALA34 as a starting terminus. 32: Identified residue ALA49 as a ending terminus. 32: Start terminus ALA-34: NH3+ 32: End terminus ALA-49: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 170 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 32: The Gromos53a6 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6 (90 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 21 acceptors were found. 32: There are 30 hydrogen bonds 32: Will use HISE for residue 60 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS60 32: NE285 32: CYS62 SG98 0.803 32: Making bonds... 32: Number of bonds was 161, now 156 32: Marked 35 virtual sites 32: Added 4 dummy masses 32: Added 10 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 232 pairs 32: Before cleaning: 306 dihedrals 32: Making cmap torsions... 32: There are 78 dihedrals, 82 impropers, 231 angles 32: 232 pairs, 156 bonds and 33 virtual sites 32: Total mass 1662.887 a.m.u. 32: Total charge -0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 117 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (117 atoms, 16 residues) 32: Identified residue LYS50 as a starting terminus. 32: Identified residue PRO65 as a ending terminus. 32: Start terminus LYS-50: NH3+ 32: End terminus PRO-65: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 152 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 32: The Gromos53a6 force field and the spc water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7 (67 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 25 donors and 23 acceptors were found. 32: There are 41 hydrogen bonds 32: Will use HISE for residue 8 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS3 HIS8 32: SG9 NE251 32: HIS8 NE251 1.055 32: MET12 SD83 0.763 0.990 32: Making bonds... 32: Number of bonds was 174, now 169 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 267 pairs 32: Before cleaning: 312 dihedrals 32: Making cmap torsions... 32: There are 90 dihedrals, 79 impropers, 245 angles 32: 267 pairs, 169 bonds and 0 virtual sites 32: Total mass 1846.116 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 128 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (128 atoms, 16 residues) 32: Identified residue ALA2 as a starting terminus. 32: Identified residue SER17 as a ending terminus. 32: Start terminus ALA-2: NH3+ 32: End terminus SER-17: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 167 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 32: The Gromos53a6 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8 (102 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 30 donors and 22 acceptors were found. 32: There are 36 hydrogen bonds 32: Will use HISE for residue 29 32: Will use HISE for residue 32 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS27 HIS29 32: SG90 NE2111 32: HIS29 NE2111 0.987 32: HIS32 NE2135 1.590 1.155 32: Making bonds... 32: Number of bonds was 220, now 215 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 273 pairs 32: Before cleaning: 443 dihedrals 32: Making cmap torsions... 32: There are 93 dihedrals, 138 impropers, 324 angles 32: 273 pairs, 215 bonds and 0 virtual sites 32: Total mass 2088.361 a.m.u. 32: Total charge 1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 149 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (149 atoms, 16 residues) 32: Identified residue THR18 as a starting terminus. 32: Identified residue PHE33 as a ending terminus. 32: Start terminus THR-18: NH3+ 32: End terminus PHE-33: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 206 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 32: The Gromos53a6 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9 (131 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 22 acceptors were found. 32: There are 26 hydrogen bonds 32: Will use HISE for residue 45 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS45 32: NE295 32: MET46 SD102 1.078 32: Making bonds... 32: Number of bonds was 181, now 176 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 242 pairs 32: Before cleaning: 356 dihedrals 32: Making cmap torsions... 32: There are 81 dihedrals, 104 impropers, 264 angles 32: 242 pairs, 176 bonds and 0 virtual sites 32: Total mass 1861.132 a.m.u. 32: Total charge -1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 132 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (132 atoms, 16 residues) 32: Identified residue ALA34 as a starting terminus. 32: Identified residue ALA49 as a ending terminus. 32: Start terminus ALA-34: NH3+ 32: End terminus ALA-49: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 170 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 32: The Gromos53a6 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10 (73 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 21 acceptors were found. 32: There are 30 hydrogen bonds 32: Will use HISE for residue 60 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS60 32: NE285 32: CYS62 SG98 0.803 32: Making bonds... 32: Number of bonds was 161, now 156 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 232 pairs 32: Before cleaning: 306 dihedrals 32: Making cmap torsions... 32: There are 78 dihedrals, 82 impropers, 231 angles 32: 232 pairs, 156 bonds and 0 virtual sites 32: Total mass 1662.887 a.m.u. 32: Total charge -0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 117 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (117 atoms, 16 residues) 32: Identified residue LYS50 as a starting terminus. 32: Identified residue PRO65 as a ending terminus. 32: Start terminus LYS-50: NH3+ 32: End terminus PRO-65: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 152 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 32: The Gromos53a6 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11 (82 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 25 donors and 23 acceptors were found. 32: There are 41 hydrogen bonds 32: Will use HISE for residue 8 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS3 HIS8 32: SG9 NE251 32: HIS8 NE251 1.055 32: MET12 SD83 0.763 0.990 32: Making bonds... 32: Number of bonds was 174, now 169 32: Marked 39 virtual sites 32: Added 4 dummy masses 32: Added 8 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 267 pairs 32: Before cleaning: 312 dihedrals 32: Making cmap torsions... 32: There are 90 dihedrals, 79 impropers, 245 angles 32: 267 pairs, 169 bonds and 39 virtual sites 32: Total mass 1846.116 a.m.u. 32: Total charge 0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 128 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (128 atoms, 16 residues) 32: Identified residue ALA2 as a starting terminus. 32: Identified residue SER17 as a ending terminus. 32: Start terminus ALA-2: NH3+ 32: End terminus SER-17: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 167 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 32: The Gromos53a6 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12 (104 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 30 donors and 22 acceptors were found. 32: There are 36 hydrogen bonds 32: Will use HISE for residue 29 32: Will use HISE for residue 32 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: CYS27 HIS29 32: SG90 NE2111 32: HIS29 NE2111 0.987 32: HIS32 NE2135 1.590 1.155 32: Making bonds... 32: Number of bonds was 220, now 215 32: Marked 57 virtual sites 32: Added 4 dummy masses 32: Added 10 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 273 pairs 32: Before cleaning: 443 dihedrals 32: Making cmap torsions... 32: There are 93 dihedrals, 138 impropers, 324 angles 32: 273 pairs, 215 bonds and 55 virtual sites 32: Total mass 2088.361 a.m.u. 32: Total charge 1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 149 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (149 atoms, 16 residues) 32: Identified residue THR18 as a starting terminus. 32: Identified residue PHE33 as a ending terminus. 32: Start terminus THR-18: NH3+ 32: End terminus PHE-33: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 206 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 32: The Gromos53a6 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13 (96 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 22 acceptors were found. 32: There are 26 hydrogen bonds 32: Will use HISE for residue 45 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS45 32: NE295 32: MET46 SD102 1.078 32: Making bonds... 32: Number of bonds was 181, now 176 32: Marked 38 virtual sites 32: Added 4 dummy masses 32: Added 8 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 242 pairs 32: Before cleaning: 356 dihedrals 32: Making cmap torsions... 32: There are 81 dihedrals, 104 impropers, 264 angles 32: 242 pairs, 176 bonds and 38 virtual sites 32: Total mass 1861.132 a.m.u. 32: Total charge -1.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 132 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (132 atoms, 16 residues) 32: Identified residue ALA34 as a starting terminus. 32: Identified residue ALA49 as a ending terminus. 32: Start terminus ALA-34: NH3+ 32: End terminus ALA-49: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 170 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 32: The Gromos53a6 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14 (90 ms) 32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.r2b 32: All occupancies are one 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/atomtypes.atp 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.rtp 32: Using default: not generating all possible dihedrals 32: Using default: excluding 3 bonded neighbors 32: Using default: generating 1,4 H--H interactions 32: Using default: removing proper dihedrals found on the same bond as a proper dihedral 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.hdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.n.tdb 32: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/gromos53a6.ff/aminoacids.c.tdb 32: Analysing hydrogen-bonding network for automated assignment of histidine 32: protonation. 22 donors and 21 acceptors were found. 32: There are 30 hydrogen bonds 32: Will use HISE for residue 60 32: 8 out of 8 lines of specbond.dat converted successfully 32: Special Atom Distance matrix: 32: HIS60 32: NE285 32: CYS62 SG98 0.803 32: Making bonds... 32: Number of bonds was 161, now 156 32: Marked 35 virtual sites 32: Added 4 dummy masses 32: Added 10 new constraints 32: Generating angles, dihedrals and pairs... 32: 32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom H used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: 32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 32: to an entry in the topology database, but the atom O used in 32: an interaction of type angle in that entry is not found in the 32: input file. Perhaps your atom and/or residue naming needs to be 32: fixed. 32: 32: 32: Before cleaning: 232 pairs 32: Before cleaning: 306 dihedrals 32: Making cmap torsions... 32: There are 78 dihedrals, 82 impropers, 231 angles 32: 232 pairs, 156 bonds and 33 virtual sites 32: Total mass 1662.887 a.m.u. 32: Total charge -0.000 e 32: Writing topology 32: 32: Writing coordinate file... 32: 32: Using the Gromos53a6 force field in directory gromos53a6.ff 32: 32: going to rename gromos53a6.ff/aminoacids.r2b 32: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 32: Analyzing pdb file 32: Splitting chemical chains based on TER records or chain id changing. 32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 32: 32: chain #res #atoms 32: 1 ' ' 16 117 32: 32: Reading residue database... (Gromos53a6) 32: Processing chain 1 (117 atoms, 16 residues) 32: Identified residue LYS50 as a starting terminus. 32: Identified residue PRO65 as a ending terminus. 32: Start terminus LYS-50: NH3+ 32: End terminus PRO-65: COO- 32: Checking for duplicate atoms.... 32: Generating any missing hydrogen atoms and/or adding termini. 32: Now there are 16 residues with 152 atoms 32: --------- PLEASE NOTE ------------ 32: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 32: The Gromos53a6 force field and the spce water model are used. 32: --------- ETON ESAELP ------------ 32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15 (73 ms) 32: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest (1475 ms total) 32: 32: [----------] Global test environment tear-down 32: [==========] 32 tests from 2 test cases ran. (2916 ms total) 32: [ PASSED ] 32 tests. 32/54 Test #32: Pdb2gmx2Test ........................ Passed 2.96 sec test 33 Start 33: Pdb2gmx3Test 33: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/pdb2gmx3-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/Pdb2gmx3Test.xml" 33: Test timeout computed to be: 30 33: [==========] Running 28 tests from 4 test cases. 33: [----------] Global test environment set-up. 33: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest 33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 25 donors and 23 acceptors were found. 33: There are 41 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 HIS8 33: SG9 NE251 33: HIS8 NE251 1.055 33: MET12 SD83 0.763 0.990 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.arn 33: Making bonds... 33: Number of bonds was 255, now 254 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 653 pairs 33: Before cleaning: 691 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 691 dihedrals, 51 impropers, 457 angles 33: 650 pairs, 254 bonds and 0 virtual sites 33: Total mass 1846.132 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 33: 33: going to rename amber99sb-ildn.ff/aminoacids.r2b 33: going to rename amber99sb-ildn.ff/dna.r2b 33: going to rename amber99sb-ildn.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 128 33: 33: Reading residue database... (Amber99sb-ildn) 33: Processing chain 1 (128 atoms, 16 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 252 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 33: The Amber99sb-ildn force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0 (154 ms) 33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 30 donors and 22 acceptors were found. 33: There are 36 hydrogen bonds 33: Will use HISE for residue 29 33: Will use HISE for residue 32 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS27 HIS29 33: SG90 NE2111 33: HIS29 NE2111 0.987 33: HIS32 NE2135 1.590 1.155 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.arn 33: Making bonds... 33: Number of bonds was 291, now 290 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 748 pairs 33: Before cleaning: 788 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 788 dihedrals, 72 impropers, 516 angles 33: 736 pairs, 290 bonds and 0 virtual sites 33: Total mass 2088.366 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 33: 33: going to rename amber99sb-ildn.ff/aminoacids.r2b 33: going to rename amber99sb-ildn.ff/dna.r2b 33: going to rename amber99sb-ildn.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 149 33: 33: Reading residue database... (Amber99sb-ildn) 33: Processing chain 1 (149 atoms, 16 residues) 33: Identified residue THR18 as a starting terminus. 33: Identified residue PHE33 as a ending terminus. 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 281 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 33: The Amber99sb-ildn force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1 (143 ms) 33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 22 donors and 22 acceptors were found. 33: There are 26 hydrogen bonds 33: Will use HISE for residue 45 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: HIS45 33: NE295 33: MET46 SD102 1.078 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.arn 33: Making bonds... 33: Number of bonds was 262, now 261 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 676 pairs 33: Before cleaning: 727 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 727 dihedrals, 56 impropers, 472 angles 33: 667 pairs, 261 bonds and 0 virtual sites 33: Total mass 1861.124 a.m.u. 33: Total charge -1.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 33: 33: going to rename amber99sb-ildn.ff/aminoacids.r2b 33: going to rename amber99sb-ildn.ff/dna.r2b 33: going to rename amber99sb-ildn.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 132 33: 33: Reading residue database... (Amber99sb-ildn) 33: Processing chain 1 (132 atoms, 16 residues) 33: Identified residue ALA34 as a starting terminus. 33: Identified residue ALA49 as a ending terminus. 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 255 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 33: The Amber99sb-ildn force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2 (124 ms) 33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 22 donors and 21 acceptors were found. 33: There are 30 hydrogen bonds 33: Will use HISE for residue 60 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: HIS60 33: NE285 33: CYS62 SG98 0.803 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.arn 33: Making bonds... 33: Number of bonds was 233, now 232 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 603 pairs 33: Before cleaning: 634 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 634 dihedrals, 48 impropers, 419 angles 33: 597 pairs, 232 bonds and 0 virtual sites 33: Total mass 1662.888 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 33: 33: going to rename amber99sb-ildn.ff/aminoacids.r2b 33: going to rename amber99sb-ildn.ff/dna.r2b 33: going to rename amber99sb-ildn.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 117 33: 33: Reading residue database... (Amber99sb-ildn) 33: Processing chain 1 (117 atoms, 16 residues) 33: Identified residue LYS50 as a starting terminus. 33: Identified residue PRO65 as a ending terminus. 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 228 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 33: The Amber99sb-ildn force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3 (95 ms) 33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 25 donors and 23 acceptors were found. 33: There are 41 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 HIS8 33: SG9 NE251 33: HIS8 NE251 1.055 33: MET12 SD83 0.763 0.990 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.arn 33: Making bonds... 33: Number of bonds was 255, now 254 33: Marked 124 virtual sites 33: Added 16 dummy masses 33: Added 26 new constraints 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 653 pairs 33: Before cleaning: 691 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 691 dihedrals, 51 impropers, 457 angles 33: 650 pairs, 254 bonds and 130 virtual sites 33: Total mass 1846.132 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 33: 33: going to rename amber99sb-ildn.ff/aminoacids.r2b 33: going to rename amber99sb-ildn.ff/dna.r2b 33: going to rename amber99sb-ildn.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 128 33: 33: Reading residue database... (Amber99sb-ildn) 33: Processing chain 1 (128 atoms, 16 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 252 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 33: The Amber99sb-ildn force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4 (115 ms) 33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 30 donors and 22 acceptors were found. 33: There are 36 hydrogen bonds 33: Will use HISE for residue 29 33: Will use HISE for residue 32 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS27 HIS29 33: SG90 NE2111 33: HIS29 NE2111 0.987 33: HIS32 NE2135 1.590 1.155 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.arn 33: Making bonds... 33: Number of bonds was 291, now 290 33: Marked 132 virtual sites 33: Added 10 dummy masses 33: Added 19 new constraints 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 748 pairs 33: Before cleaning: 788 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 788 dihedrals, 72 impropers, 516 angles 33: 736 pairs, 290 bonds and 133 virtual sites 33: Total mass 2088.366 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 33: 33: going to rename amber99sb-ildn.ff/aminoacids.r2b 33: going to rename amber99sb-ildn.ff/dna.r2b 33: going to rename amber99sb-ildn.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 149 33: 33: Reading residue database... (Amber99sb-ildn) 33: Processing chain 1 (149 atoms, 16 residues) 33: Identified residue THR18 as a starting terminus. 33: Identified residue PHE33 as a ending terminus. 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 281 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 33: The Amber99sb-ildn force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5 (139 ms) 33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 22 donors and 22 acceptors were found. 33: There are 26 hydrogen bonds 33: Will use HISE for residue 45 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: HIS45 33: NE295 33: MET46 SD102 1.078 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.arn 33: Making bonds... 33: Number of bonds was 262, now 261 33: Marked 123 virtual sites 33: Added 22 dummy masses 33: Added 35 new constraints 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 676 pairs 33: Before cleaning: 727 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 727 dihedrals, 56 impropers, 472 angles 33: 667 pairs, 261 bonds and 132 virtual sites 33: Total mass 1861.124 a.m.u. 33: Total charge -1.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 33: 33: going to rename amber99sb-ildn.ff/aminoacids.r2b 33: going to rename amber99sb-ildn.ff/dna.r2b 33: going to rename amber99sb-ildn.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 132 33: 33: Reading residue database... (Amber99sb-ildn) 33: Processing chain 1 (132 atoms, 16 residues) 33: Identified residue ALA34 as a starting terminus. 33: Identified residue ALA49 as a ending terminus. 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 255 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 33: The Amber99sb-ildn force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6 (145 ms) 33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 22 donors and 21 acceptors were found. 33: There are 30 hydrogen bonds 33: Will use HISE for residue 60 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: HIS60 33: NE285 33: CYS62 SG98 0.803 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/amber99sb-ildn.ff/rna.arn 33: Making bonds... 33: Number of bonds was 233, now 232 33: Marked 111 virtual sites 33: Added 18 dummy masses 33: Added 31 new constraints 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 603 pairs 33: Before cleaning: 634 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 634 dihedrals, 48 impropers, 419 angles 33: 597 pairs, 232 bonds and 116 virtual sites 33: Total mass 1662.888 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 33: 33: going to rename amber99sb-ildn.ff/aminoacids.r2b 33: going to rename amber99sb-ildn.ff/dna.r2b 33: going to rename amber99sb-ildn.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 117 33: 33: Reading residue database... (Amber99sb-ildn) 33: Processing chain 1 (117 atoms, 16 residues) 33: Identified residue LYS50 as a starting terminus. 33: Identified residue PRO65 as a ending terminus. 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 228 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 33: The Amber99sb-ildn force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7 (145 ms) 33: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest (1060 ms total) 33: 33: [----------] 8 tests from ForCharmm27/Pdb2gmxTest 33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 25 donors and 23 acceptors were found. 33: There are 41 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 HIS8 33: SG9 NE251 33: HIS8 NE251 1.055 33: MET12 SD83 0.763 0.990 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 254, now 254 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 653 pairs 33: Before cleaning: 663 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 14 cmap torsion pairs 33: There are 663 dihedrals, 48 impropers, 457 angles 33: 650 pairs, 254 bonds and 0 virtual sites 33: Total mass 1846.115 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 128 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 (128 atoms, 16 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 252 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0 (115 ms) 33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 30 donors and 22 acceptors were found. 33: There are 36 hydrogen bonds 33: Will use HISE for residue 29 33: Will use HISE for residue 32 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS27 HIS29 33: SG90 NE2111 33: HIS29 NE2111 0.987 33: HIS32 NE2135 1.590 1.155 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 290, now 290 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 748 pairs 33: Before cleaning: 778 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 14 cmap torsion pairs 33: There are 778 dihedrals, 49 impropers, 516 angles 33: 736 pairs, 290 bonds and 0 virtual sites 33: Total mass 2088.361 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 149 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 (149 atoms, 16 residues) 33: Identified residue THR18 as a starting terminus. 33: Identified residue PHE33 as a ending terminus. 33: Start terminus THR-18: NH3+ 33: End terminus PHE-33: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 281 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1 (123 ms) 33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 22 donors and 22 acceptors were found. 33: There are 26 hydrogen bonds 33: Will use HISE for residue 45 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: HIS45 33: NE295 33: MET46 SD102 1.078 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 261, now 261 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 676 pairs 33: Before cleaning: 696 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 14 cmap torsion pairs 33: There are 696 dihedrals, 39 impropers, 472 angles 33: 667 pairs, 261 bonds and 0 virtual sites 33: Total mass 1861.130 a.m.u. 33: Total charge -1.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 132 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 (132 atoms, 16 residues) 33: Identified residue ALA34 as a starting terminus. 33: Identified residue ALA49 as a ending terminus. 33: Start terminus ALA-34: NH3+ 33: End terminus ALA-49: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 255 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2 (111 ms) 33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 22 donors and 21 acceptors were found. 33: There are 30 hydrogen bonds 33: Will use HISE for residue 60 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: HIS60 33: NE285 33: CYS62 SG98 0.803 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 232, now 232 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 603 pairs 33: Before cleaning: 618 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 14 cmap torsion pairs 33: There are 618 dihedrals, 38 impropers, 419 angles 33: 597 pairs, 232 bonds and 0 virtual sites 33: Total mass 1662.885 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 117 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 (117 atoms, 16 residues) 33: Identified residue LYS50 as a starting terminus. 33: Identified residue PRO65 as a ending terminus. 33: Start terminus LYS-50: NH3+ 33: End terminus PRO-65: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 228 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3 (113 ms) 33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 25 donors and 23 acceptors were found. 33: There are 41 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 HIS8 33: SG9 NE251 33: HIS8 NE251 1.055 33: MET12 SD83 0.763 0.990 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 254, now 254 33: Marked 124 virtual sites 33: Added 16 dummy masses 33: Added 26 new constraints 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 653 pairs 33: Before cleaning: 663 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 14 cmap torsion pairs 33: There are 663 dihedrals, 48 impropers, 457 angles 33: 650 pairs, 254 bonds and 130 virtual sites 33: Total mass 1846.115 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 128 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 (128 atoms, 16 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 252 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4 (132 ms) 33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 30 donors and 22 acceptors were found. 33: There are 36 hydrogen bonds 33: Will use HISE for residue 29 33: Will use HISE for residue 32 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS27 HIS29 33: SG90 NE2111 33: HIS29 NE2111 0.987 33: HIS32 NE2135 1.590 1.155 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 290, now 290 33: Marked 132 virtual sites 33: Added 10 dummy masses 33: Added 19 new constraints 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 748 pairs 33: Before cleaning: 778 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 14 cmap torsion pairs 33: There are 778 dihedrals, 49 impropers, 516 angles 33: 736 pairs, 290 bonds and 133 virtual sites 33: Total mass 2088.361 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 149 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 (149 atoms, 16 residues) 33: Identified residue THR18 as a starting terminus. 33: Identified residue PHE33 as a ending terminus. 33: Start terminus THR-18: NH3+ 33: End terminus PHE-33: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 281 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5 (163 ms) 33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 22 donors and 22 acceptors were found. 33: There are 26 hydrogen bonds 33: Will use HISE for residue 45 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: HIS45 33: NE295 33: MET46 SD102 1.078 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 261, now 261 33: Marked 123 virtual sites 33: Added 22 dummy masses 33: Added 35 new constraints 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 676 pairs 33: Before cleaning: 696 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 14 cmap torsion pairs 33: There are 696 dihedrals, 39 impropers, 472 angles 33: 667 pairs, 261 bonds and 132 virtual sites 33: Total mass 1861.130 a.m.u. 33: Total charge -1.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 132 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 (132 atoms, 16 residues) 33: Identified residue ALA34 as a starting terminus. 33: Identified residue ALA49 as a ending terminus. 33: Start terminus ALA-34: NH3+ 33: End terminus ALA-49: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 255 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6 (105 ms) 33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 22 donors and 21 acceptors were found. 33: There are 30 hydrogen bonds 33: Will use HISE for residue 60 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: HIS60 33: NE285 33: CYS62 SG98 0.803 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 232, now 232 33: Marked 111 virtual sites 33: Added 18 dummy masses 33: Added 31 new constraints 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 603 pairs 33: Before cleaning: 618 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 14 cmap torsion pairs 33: There are 618 dihedrals, 38 impropers, 419 angles 33: 597 pairs, 232 bonds and 116 virtual sites 33: Total mass 1662.885 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 33: 33: chain #res #atoms 33: 1 ' ' 16 117 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 (117 atoms, 16 residues) 33: Identified residue LYS50 as a starting terminus. 33: Identified residue PRO65 as a ending terminus. 33: Start terminus LYS-50: NH3+ 33: End terminus PRO-65: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 228 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7 (135 ms) 33: [----------] 8 tests from ForCharmm27/Pdb2gmxTest (997 ms total) 33: 33: [----------] 8 tests from ChainSep/Pdb2gmxTest 33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 25 donors and 23 acceptors were found. 33: There are 41 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 HIS8 33: SG9 NE251 33: HIS8 NE251 1.055 33: MET12 SD83 0.763 0.990 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 258, now 258 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 651 pairs 33: Before cleaning: 661 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 10 cmap torsion pairs 33: There are 661 dihedrals, 46 impropers, 463 angles 33: 648 pairs, 258 bonds and 0 virtual sites 33: Total mass 1882.146 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on changing chain id only (ignoring TER records). 33: 33: Merged chains into joint molecule definitions at 2 places. 33: 33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 33: 33: chain #res #atoms 33: 1 'A' 16 127 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (127 atoms, 16 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue GLU5 as a ending terminus. 33: Identified residue PHE6 as a starting terminus. 33: Identified residue MET12 as a ending terminus. 33: Identified residue ASN13 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus GLU-5: COO- 33: Start terminus PHE-6: NH3+ 33: End terminus MET-12: COO- 33: Start terminus ASN-13: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 258 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0 (112 ms) 33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 50, now 50 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 123 pairs 33: Before cleaning: 123 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 2 cmap torsion pairs 33: There are 123 dihedrals, 9 impropers, 88 angles 33: 123 pairs, 50 bonds and 0 virtual sites 33: Total mass 434.421 a.m.u. 33: Total charge -2.000 e 33: Writing topology 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 10 donors and 7 acceptors were found. 33: There are 7 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: HIS8 33: NE223 33: MET12 SD55 0.990 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 125, now 125 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 317 pairs 33: Before cleaning: 322 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 5 cmap torsion pairs 33: There are 322 dihedrals, 19 impropers, 227 angles 33: 314 pairs, 125 bonds and 0 virtual sites 33: Total mass 846.083 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 83, now 83 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 211 pairs 33: Before cleaning: 216 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 3 cmap torsion pairs 33: There are 216 dihedrals, 18 impropers, 148 angles 33: 211 pairs, 83 bonds and 0 virtual sites 33: Total mass 601.643 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: Now there are 258 atoms and 16 residues 33: Total mass in system 1882.146 a.m.u. 33: Total charge in system 0.000 e 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on changing chain id only (ignoring TER records). 33: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 33: 33: chain #res #atoms 33: 1 'A' 4 28 33: 2 'B' 7 58 33: 3 'C' 5 41 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (28 atoms, 4 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue GLU5 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus GLU-5: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 4 residues with 51 atoms 33: Chain time... 33: Processing chain 2 'B' (58 atoms, 7 residues) 33: Identified residue PHE6 as a starting terminus. 33: Identified residue MET12 as a ending terminus. 33: Start terminus PHE-6: NH3+ 33: End terminus MET-12: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 7 residues with 124 atoms 33: Chain time... 33: Processing chain 3 'C' (41 atoms, 5 residues) 33: Identified residue ASN13 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ASN-13: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 5 residues with 83 atoms 33: Chain time... 33: Including chain 1 in system: 51 atoms 4 residues 33: Including chain 2 in system: 124 atoms 7 residues 33: Including chain 3 in system: 83 atoms 5 residues 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1 (95 ms) 33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 25 donors and 23 acceptors were found. 33: There are 41 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 HIS8 33: SG9 NE251 33: HIS8 NE251 1.055 33: MET12 SD83 0.763 0.990 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 258, now 258 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 651 pairs 33: Before cleaning: 661 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 10 cmap torsion pairs 33: There are 661 dihedrals, 46 impropers, 463 angles 33: 648 pairs, 258 bonds and 0 virtual sites 33: Total mass 1882.146 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records only (ignoring chain id). 33: 33: Merged chains into joint molecule definitions at 2 places. 33: 33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 33: 33: chain #res #atoms 33: 1 'A' 16 127 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (127 atoms, 16 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue ILE9 as a ending terminus. 33: Identified residue LYS10 as a starting terminus. 33: Identified residue MET12 as a ending terminus. 33: Identified residue ASN13 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus ILE-9: COO- 33: Start terminus LYS-10: NH3+ 33: End terminus MET-12: COO- 33: Start terminus ASN-13: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 258 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2 (121 ms) 33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 10 donors and 12 acceptors were found. 33: There are 13 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 33: SG9 33: HIS8 NE251 1.055 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 115, now 115 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 288 pairs 33: Before cleaning: 293 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 6 cmap torsion pairs 33: There are 293 dihedrals, 23 impropers, 203 angles 33: 285 pairs, 115 bonds and 0 virtual sites 33: Total mass 888.952 a.m.u. 33: Total charge -2.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 60, now 60 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 152 pairs 33: Before cleaning: 152 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 152 dihedrals, 5 impropers, 112 angles 33: 152 pairs, 60 bonds and 0 virtual sites 33: Total mass 391.552 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 83, now 83 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 211 pairs 33: Before cleaning: 216 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 3 cmap torsion pairs 33: There are 216 dihedrals, 18 impropers, 148 angles 33: 211 pairs, 83 bonds and 0 virtual sites 33: Total mass 601.643 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: Now there are 258 atoms and 16 residues 33: Total mass in system 1882.146 a.m.u. 33: Total charge in system 0.000 e 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records only (ignoring chain id). 33: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 33: 33: chain #res #atoms 33: 1 'A' 8 61 33: 2 'B' 3 25 33: 3 'C' 5 41 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (61 atoms, 8 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue ILE9 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus ILE-9: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 8 residues with 114 atoms 33: Chain time... 33: Processing chain 2 'B' (25 atoms, 3 residues) 33: Identified residue LYS10 as a starting terminus. 33: Identified residue MET12 as a ending terminus. 33: Start terminus LYS-10: NH3+ 33: End terminus MET-12: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 61 atoms 33: Chain time... 33: Processing chain 3 'C' (41 atoms, 5 residues) 33: Identified residue ASN13 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ASN-13: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 5 residues with 83 atoms 33: Chain time... 33: Including chain 1 in system: 114 atoms 8 residues 33: Including chain 2 in system: 61 atoms 3 residues 33: Including chain 3 in system: 83 atoms 5 residues 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3 (97 ms) 33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 25 donors and 23 acceptors were found. 33: There are 41 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 HIS8 33: SG9 NE251 33: HIS8 NE251 1.055 33: MET12 SD83 0.763 0.990 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 260, now 260 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 650 pairs 33: Before cleaning: 660 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 8 cmap torsion pairs 33: There are 660 dihedrals, 45 impropers, 466 angles 33: 647 pairs, 260 bonds and 0 virtual sites 33: Total mass 1900.162 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: 33: Merged chains into joint molecule definitions at 3 places. 33: 33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 33: 33: chain #res #atoms 33: 1 'A' 16 127 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (127 atoms, 16 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue GLU5 as a ending terminus. 33: Identified residue PHE6 as a starting terminus. 33: Identified residue ILE9 as a ending terminus. 33: Identified residue LYS10 as a starting terminus. 33: Identified residue MET12 as a ending terminus. 33: Identified residue ASN13 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus GLU-5: COO- 33: Start terminus PHE-6: NH3+ 33: End terminus ILE-9: COO- 33: Start terminus LYS-10: NH3+ 33: End terminus MET-12: COO- 33: Start terminus ASN-13: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 261 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4 (113 ms) 33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 50, now 50 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 123 pairs 33: Before cleaning: 123 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 2 cmap torsion pairs 33: There are 123 dihedrals, 9 impropers, 88 angles 33: 123 pairs, 50 bonds and 0 virtual sites 33: Total mass 434.421 a.m.u. 33: Total charge -2.000 e 33: Writing topology 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 6 donors and 4 acceptors were found. 33: There are 3 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 67, now 67 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 164 pairs 33: Before cleaning: 169 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 2 cmap torsion pairs 33: There are 169 dihedrals, 13 impropers, 118 angles 33: 161 pairs, 67 bonds and 0 virtual sites 33: Total mass 472.547 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 60, now 60 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 152 pairs 33: Before cleaning: 152 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 152 dihedrals, 5 impropers, 112 angles 33: 152 pairs, 60 bonds and 0 virtual sites 33: Total mass 391.552 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 83, now 83 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 211 pairs 33: Before cleaning: 216 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 3 cmap torsion pairs 33: There are 216 dihedrals, 18 impropers, 148 angles 33: 211 pairs, 83 bonds and 0 virtual sites 33: Total mass 601.643 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: Now there are 261 atoms and 16 residues 33: Total mass in system 1900.162 a.m.u. 33: Total charge in system 0.000 e 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: WARNING: Chain identifier 'B' is used in two non-sequential blocks. 33: They will be treated as separate chains unless you reorder your file. 33: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms 33: 33: chain #res #atoms 33: 1 'A' 4 28 33: 2 'B' 4 33 33: 3 'B' 3 25 33: 4 'C' 5 41 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (28 atoms, 4 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue GLU5 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus GLU-5: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 4 residues with 51 atoms 33: Chain time... 33: Processing chain 2 'B' (33 atoms, 4 residues) 33: Identified residue PHE6 as a starting terminus. 33: Identified residue ILE9 as a ending terminus. 33: Start terminus PHE-6: NH3+ 33: End terminus ILE-9: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 4 residues with 66 atoms 33: Chain time... 33: Processing chain 3 'B' (25 atoms, 3 residues) 33: Identified residue LYS10 as a starting terminus. 33: Identified residue MET12 as a ending terminus. 33: Start terminus LYS-10: NH3+ 33: End terminus MET-12: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 61 atoms 33: Chain time... 33: Processing chain 4 'C' (41 atoms, 5 residues) 33: Identified residue ASN13 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ASN-13: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 5 residues with 83 atoms 33: Chain time... 33: Including chain 1 in system: 51 atoms 4 residues 33: Including chain 2 in system: 66 atoms 4 residues 33: Including chain 3 in system: 61 atoms 3 residues 33: Including chain 4 in system: 83 atoms 5 residues 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5 (94 ms) 33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 25 donors and 23 acceptors were found. 33: There are 41 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 HIS8 33: SG9 NE251 33: HIS8 NE251 1.055 33: MET12 SD83 0.763 0.990 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 256, now 256 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 652 pairs 33: Before cleaning: 662 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 12 cmap torsion pairs 33: There are 662 dihedrals, 47 impropers, 460 angles 33: 649 pairs, 256 bonds and 0 virtual sites 33: Total mass 1864.131 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records and chain id changing. 33: 33: Merged chains into joint molecule definitions at 1 places. 33: 33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 33: 33: chain #res #atoms 33: 1 'A' 16 127 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (127 atoms, 16 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue MET12 as a ending terminus. 33: Identified residue ASN13 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus MET-12: COO- 33: Start terminus ASN-13: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 16 residues with 255 atoms 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6 (101 ms) 33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: Analysing hydrogen-bonding network for automated assignment of histidine 33: protonation. 14 donors and 15 acceptors were found. 33: There are 20 hydrogen bonds 33: Will use HISE for residue 8 33: 8 out of 8 lines of specbond.dat converted successfully 33: Special Atom Distance matrix: 33: CYS3 HIS8 33: SG9 NE251 33: HIS8 NE251 1.055 33: MET12 SD83 0.763 0.990 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 173, now 173 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 441 pairs 33: Before cleaning: 446 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 9 cmap torsion pairs 33: There are 446 dihedrals, 29 impropers, 312 angles 33: 438 pairs, 173 bonds and 0 virtual sites 33: Total mass 1262.488 a.m.u. 33: Total charge -1.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 83, now 83 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 211 pairs 33: Before cleaning: 216 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 3 cmap torsion pairs 33: There are 216 dihedrals, 18 impropers, 148 angles 33: 211 pairs, 83 bonds and 0 virtual sites 33: Total mass 601.643 a.m.u. 33: Total charge 1.000 e 33: Writing topology 33: Now there are 255 atoms and 16 residues 33: Total mass in system 1864.131 a.m.u. 33: Total charge in system 0.000 e 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records and chain id changing. 33: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms 33: 33: chain #res #atoms 33: 1 'A' 11 86 33: 2 'C' 5 41 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (86 atoms, 11 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue MET12 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus MET-12: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 11 residues with 172 atoms 33: Chain time... 33: Processing chain 2 'C' (41 atoms, 5 residues) 33: Identified residue ASN13 as a starting terminus. 33: Identified residue SER17 as a ending terminus. 33: Start terminus ASN-13: NH3+ 33: End terminus SER-17: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 5 residues with 83 atoms 33: Chain time... 33: Including chain 1 in system: 172 atoms 11 residues 33: Including chain 2 in system: 83 atoms 5 residues 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7 (94 ms) 33: [----------] 8 tests from ChainSep/Pdb2gmxTest (827 ms total) 33: 33: [----------] 4 tests from ChainChanges/Pdb2gmxTest 33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 35, now 35 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 83 pairs 33: Before cleaning: 83 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 83 dihedrals, 6 impropers, 61 angles 33: 83 pairs, 35 bonds and 0 virtual sites 33: Total mass 306.314 a.m.u. 33: Total charge -1.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 58, now 58 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 145 pairs 33: Before cleaning: 150 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 150 dihedrals, 5 impropers, 103 angles 33: 142 pairs, 58 bonds and 0 virtual sites 33: Total mass 404.468 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: Now there are 93 atoms and 6 residues 33: Total mass in system 710.782 a.m.u. 33: Total charge in system -1.000 e 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/two-fragments.pdb... 33: Read 'Fragments of peptides and ions', 47 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on changing chain id only (ignoring TER records). 33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 33: 33: chain #res #atoms 33: 1 'A' 3 19 33: 2 'B' 3 28 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (19 atoms, 3 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue ASP4 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus ASP-4: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 36 atoms 33: Chain time... 33: Processing chain 2 'B' (28 atoms, 3 residues) 33: Identified residue THR18 as a starting terminus. 33: Identified residue TRP20 as a ending terminus. 33: Start terminus THR-18: NH3+ 33: End terminus TRP-20: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 57 atoms 33: Chain time... 33: Including chain 1 in system: 36 atoms 3 residues 33: Including chain 2 in system: 57 atoms 3 residues 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/two-fragments.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0 (89 ms) 33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 35, now 35 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 83 pairs 33: Before cleaning: 83 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 83 dihedrals, 6 impropers, 61 angles 33: 83 pairs, 35 bonds and 0 virtual sites 33: Total mass 306.314 a.m.u. 33: Total charge -1.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 58, now 58 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 145 pairs 33: Before cleaning: 150 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 150 dihedrals, 5 impropers, 103 angles 33: 142 pairs, 58 bonds and 0 virtual sites 33: Total mass 404.468 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: Now there are 93 atoms and 6 residues 33: Total mass in system 710.782 a.m.u. 33: Total charge in system -1.000 e 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/two-fragments.pdb... 33: Read 'Fragments of peptides and ions', 47 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records only (ignoring chain id). 33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 33: 33: chain #res #atoms 33: 1 'A' 3 19 33: 2 'B' 3 28 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (19 atoms, 3 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue ASP4 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus ASP-4: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 36 atoms 33: Chain time... 33: Processing chain 2 'B' (28 atoms, 3 residues) 33: Identified residue THR18 as a starting terminus. 33: Identified residue TRP20 as a ending terminus. 33: Start terminus THR-18: NH3+ 33: End terminus TRP-20: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 57 atoms 33: Chain time... 33: Including chain 1 in system: 36 atoms 3 residues 33: Including chain 2 in system: 57 atoms 3 residues 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/two-fragments.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1 (90 ms) 33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 35, now 35 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 83 pairs 33: Before cleaning: 83 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 83 dihedrals, 6 impropers, 61 angles 33: 83 pairs, 35 bonds and 0 virtual sites 33: Total mass 306.314 a.m.u. 33: Total charge -1.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 58, now 58 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 145 pairs 33: Before cleaning: 150 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 150 dihedrals, 5 impropers, 103 angles 33: 142 pairs, 58 bonds and 0 virtual sites 33: Total mass 404.468 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: Now there are 93 atoms and 6 residues 33: Total mass in system 710.782 a.m.u. 33: Total charge in system -1.000 e 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/two-fragments.pdb... 33: Read 'Fragments of peptides and ions', 47 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records or chain id changing. 33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 33: 33: chain #res #atoms 33: 1 'A' 3 19 33: 2 'B' 3 28 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (19 atoms, 3 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue ASP4 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus ASP-4: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 36 atoms 33: Chain time... 33: Processing chain 2 'B' (28 atoms, 3 residues) 33: Identified residue THR18 as a starting terminus. 33: Identified residue TRP20 as a ending terminus. 33: Start terminus THR-18: NH3+ 33: End terminus TRP-20: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 57 atoms 33: Chain time... 33: Including chain 1 in system: 36 atoms 3 residues 33: Including chain 2 in system: 57 atoms 3 residues 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/two-fragments.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2 (55 ms) 33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.r2b 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.r2b 33: All occupancies are one 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/atomtypes.atp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.rtp 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/lipids.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.hdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.n.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.c.tdb 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.c.tdb 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 35, now 35 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 83 pairs 33: Before cleaning: 83 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 83 dihedrals, 6 impropers, 61 angles 33: 83 pairs, 35 bonds and 0 virtual sites 33: Total mass 306.314 a.m.u. 33: Total charge -1.000 e 33: Writing topology 33: 8 out of 8 lines of specbond.dat converted successfully 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/aminoacids.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/dna.arn 33: Opening force field file /build/gromacs-5atmZb/gromacs-2020.6/share/top/charmm27.ff/rna.arn 33: Making bonds... 33: Number of bonds was 58, now 58 33: Generating angles, dihedrals and pairs... 33: Before cleaning: 145 pairs 33: Before cleaning: 150 dihedrals 33: Keeping all generated dihedrals 33: Making cmap torsions... 33: There are 1 cmap torsion pairs 33: There are 150 dihedrals, 5 impropers, 103 angles 33: 142 pairs, 58 bonds and 0 virtual sites 33: Total mass 404.468 a.m.u. 33: Total charge 0.000 e 33: Writing topology 33: Now there are 93 atoms and 6 residues 33: Total mass in system 710.782 a.m.u. 33: Total charge in system -1.000 e 33: 33: Writing coordinate file... 33: 33: Using the Charmm27 force field in directory charmm27.ff 33: 33: going to rename charmm27.ff/aminoacids.r2b 33: going to rename charmm27.ff/rna.r2b 33: Reading /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/two-fragments.pdb... 33: Read 'Fragments of peptides and ions', 47 atoms 33: Analyzing pdb file 33: Splitting chemical chains based on TER records and chain id changing. 33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 33: 33: chain #res #atoms 33: 1 'A' 3 19 33: 2 'B' 3 28 33: 33: Reading residue database... (Charmm27) 33: Processing chain 1 'A' (19 atoms, 3 residues) 33: Identified residue ALA2 as a starting terminus. 33: Identified residue ASP4 as a ending terminus. 33: Start terminus ALA-2: NH3+ 33: End terminus ASP-4: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 36 atoms 33: Chain time... 33: Processing chain 2 'B' (28 atoms, 3 residues) 33: Identified residue THR18 as a starting terminus. 33: Identified residue TRP20 as a ending terminus. 33: Start terminus THR-18: NH3+ 33: End terminus TRP-20: COO- 33: Checking for duplicate atoms.... 33: Generating any missing hydrogen atoms and/or adding termini. 33: Now there are 3 residues with 57 atoms 33: Chain time... 33: Including chain 1 in system: 36 atoms 3 residues 33: Including chain 2 in system: 57 atoms 3 residues 33: --------- PLEASE NOTE ------------ 33: You have successfully generated a topology from: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gmxpreprocess/tests/two-fragments.pdb. 33: The Charmm27 force field and the tip3p water model are used. 33: --------- ETON ESAELP ------------ 33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3 (81 ms) 33: [----------] 4 tests from ChainChanges/Pdb2gmxTest (315 ms total) 33: 33: [----------] Global test environment tear-down 33: [==========] 28 tests from 4 test cases ran. (3199 ms total) 33: [ PASSED ] 28 tests. 33/54 Test #33: Pdb2gmx3Test ........................ Passed 3.22 sec test 34 Start 34: CorrelationsTest 34: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/correlations-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/CorrelationsTest.xml" 34: Test timeout computed to be: 30 34: [==========] Running 21 tests from 3 test cases. 34: [----------] Global test environment set-up. 34: [----------] 10 tests from AutocorrTest 34: [ RUN ] AutocorrTest.EacNormal 34: [ OK ] AutocorrTest.EacNormal (337 ms) 34: [ RUN ] AutocorrTest.EacNoNormalize 34: [ OK ] AutocorrTest.EacNoNormalize (200 ms) 34: [ RUN ] AutocorrTest.EacCos 34: [ OK ] AutocorrTest.EacCos (502 ms) 34: [ RUN ] AutocorrTest.EacVector 34: [ OK ] AutocorrTest.EacVector (702 ms) 34: [ RUN ] AutocorrTest.EacRcross 34: [ OK ] AutocorrTest.EacRcross (2 ms) 34: [ RUN ] AutocorrTest.EacP0 34: [ OK ] AutocorrTest.EacP0 (788 ms) 34: [ RUN ] AutocorrTest.EacP1 34: [ OK ] AutocorrTest.EacP1 (613 ms) 34: [ RUN ] AutocorrTest.EacP2 34: [ OK ] AutocorrTest.EacP2 (1388 ms) 34: [ RUN ] AutocorrTest.EacP3 34: [ OK ] AutocorrTest.EacP3 (99 ms) 34: [ RUN ] AutocorrTest.EacP4 34: [ OK ] AutocorrTest.EacP4 (510 ms) 34: [----------] 10 tests from AutocorrTest (5146 ms total) 34: 34: [----------] 1 test from ManyAutocorrelationTest 34: [ RUN ] ManyAutocorrelationTest.Empty 34: [ OK ] ManyAutocorrelationTest.Empty (0 ms) 34: [----------] 1 test from ManyAutocorrelationTest (0 ms total) 34: 34: [----------] 10 tests from ExpfitTest 34: [ RUN ] ExpfitTest.EffnEXP1 34: [ OK ] ExpfitTest.EffnEXP1 (0 ms) 34: [ RUN ] ExpfitTest.EffnEXP2 34: [ OK ] ExpfitTest.EffnEXP2 (0 ms) 34: [ RUN ] ExpfitTest.EffnEXPEXP 34: [ OK ] ExpfitTest.EffnEXPEXP (2 ms) 34: [ RUN ] ExpfitTest.EffnEXP5 34: [ OK ] ExpfitTest.EffnEXP5 (5 ms) 34: [ RUN ] ExpfitTest.EffnEXP7 34: [ OK ] ExpfitTest.EffnEXP7 (4 ms) 34: [ RUN ] ExpfitTest.EffnEXP9 34: [ OK ] ExpfitTest.EffnEXP9 (17 ms) 34: [ RUN ] ExpfitTest.EffnERF 34: [ OK ] ExpfitTest.EffnERF (3 ms) 34: [ RUN ] ExpfitTest.EffnERREST 34: [ OK ] ExpfitTest.EffnERREST (0 ms) 34: [ RUN ] ExpfitTest.EffnVAC 34: [ OK ] ExpfitTest.EffnVAC (72 ms) 34: [ RUN ] ExpfitTest.EffnPRES 34: [ OK ] ExpfitTest.EffnPRES (15 ms) 34: [----------] 10 tests from ExpfitTest (119 ms total) 34: 34: [----------] Global test environment tear-down 34: [==========] 21 tests from 3 test cases ran. (5356 ms total) 34: [ PASSED ] 21 tests. 34/54 Test #34: CorrelationsTest .................... Passed 5.38 sec test 35 Start 35: AnalysisDataUnitTests 35: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/analysisdata-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/AnalysisDataUnitTests.xml" 35: Test timeout computed to be: 30 35: [==========] Running 69 tests from 14 test cases. 35: [----------] Global test environment set-up. 35: [----------] 3 tests from AnalysisDataInitializationTest 35: [ RUN ] AnalysisDataInitializationTest.BasicInitialization 35: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms) 35: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules 35: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms) 35: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules 35: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) 35: [----------] 3 tests from AnalysisDataInitializationTest (0 ms total) 35: 35: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = (anonymous namespace)::SimpleInputData 35: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (1 ms) 35: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (0 ms) 35: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly 35: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (1 ms) 35: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (0 ms) 35: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames 35: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (1 ms) 35: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks 35: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (0 ms) 35: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData 35: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (0 ms) 35: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks 35: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (0 ms) 35: [----------] 8 tests from AnalysisDataCommonTest/0 (3 ms total) 35: 35: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = (anonymous namespace)::DataSetsInputData 35: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (0 ms) 35: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (1 ms) 35: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly 35: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (0 ms) 35: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (0 ms) 35: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames 35: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (1 ms) 35: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks 35: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (0 ms) 35: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData 35: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (0 ms) 35: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks 35: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (1 ms) 35: [----------] 8 tests from AnalysisDataCommonTest/1 (3 ms total) 35: 35: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = (anonymous namespace)::MultipointInputData 35: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (0 ms) 35: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (1 ms) 35: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly 35: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (0 ms) 35: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (0 ms) 35: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames 35: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (1 ms) 35: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks 35: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (0 ms) 35: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData 35: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (0 ms) 35: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks 35: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (1 ms) 35: [----------] 8 tests from AnalysisDataCommonTest/2 (3 ms total) 35: 35: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = (anonymous namespace)::MultipointDataSetsInputData 35: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (0 ms) 35: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (1 ms) 35: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly 35: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (0 ms) 35: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly 35: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (0 ms) 35: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames 35: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (1 ms) 35: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks 35: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (0 ms) 35: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData 35: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (0 ms) 35: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks 35: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (1 ms) 35: [----------] 8 tests from AnalysisDataCommonTest/3 (3 ms total) 35: 35: [----------] 4 tests from AnalysisArrayDataTest 35: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly 35: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (0 ms) 35: [ RUN ] AnalysisArrayDataTest.StorageWorks 35: [ OK ] AnalysisArrayDataTest.StorageWorks (0 ms) 35: [ RUN ] AnalysisArrayDataTest.CanSetXAxis 35: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) 35: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount 35: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms) 35: [----------] 4 tests from AnalysisArrayDataTest (0 ms total) 35: 35: [----------] 6 tests from AverageModuleTest 35: [ RUN ] AverageModuleTest.BasicTest 35: [ OK ] AverageModuleTest.BasicTest (1 ms) 35: [ RUN ] AverageModuleTest.HandlesMultipointData 35: [ OK ] AverageModuleTest.HandlesMultipointData (1 ms) 35: [ RUN ] AverageModuleTest.HandlesMultipleDataSets 35: [ OK ] AverageModuleTest.HandlesMultipleDataSets (0 ms) 35: [ RUN ] AverageModuleTest.HandlesDataSetAveraging 35: [ OK ] AverageModuleTest.HandlesDataSetAveraging (1 ms) 35: [ RUN ] AverageModuleTest.CanCustomizeXAxis 35: [ OK ] AverageModuleTest.CanCustomizeXAxis (0 ms) 35: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis 35: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (1 ms) 35: [----------] 6 tests from AverageModuleTest (4 ms total) 35: 35: [----------] 2 tests from FrameAverageModuleTest 35: [ RUN ] FrameAverageModuleTest.BasicTest 35: [ OK ] FrameAverageModuleTest.BasicTest (0 ms) 35: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets 35: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (1 ms) 35: [----------] 2 tests from FrameAverageModuleTest (1 ms total) 35: 35: [----------] 7 tests from AnalysisHistogramSettingsTest 35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins 35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) 35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins 35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) 35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount 35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) 35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth 35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) 35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins 35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) 35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins 35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) 35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange 35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) 35: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total) 35: 35: [----------] 2 tests from SimpleHistogramModuleTest 35: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly 35: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (1 ms) 35: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll 35: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (1 ms) 35: [----------] 2 tests from SimpleHistogramModuleTest (2 ms total) 35: 35: [----------] 3 tests from WeightedHistogramModuleTest 35: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly 35: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (1 ms) 35: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll 35: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (1 ms) 35: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets 35: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (0 ms) 35: [----------] 3 tests from WeightedHistogramModuleTest (2 ms total) 35: 35: [----------] 3 tests from BinAverageModuleTest 35: [ RUN ] BinAverageModuleTest.ComputesCorrectly 35: [ OK ] BinAverageModuleTest.ComputesCorrectly (1 ms) 35: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll 35: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (1 ms) 35: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets 35: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (0 ms) 35: [----------] 3 tests from BinAverageModuleTest (3 ms total) 35: 35: [----------] 4 tests from AbstractAverageHistogramTest 35: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly 35: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (0 ms) 35: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram 35: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (1 ms) 35: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth 35: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (1 ms) 35: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins 35: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (1 ms) 35: [----------] 4 tests from AbstractAverageHistogramTest (3 ms total) 35: 35: [----------] 3 tests from LifetimeModuleTest 35: [ RUN ] LifetimeModuleTest.BasicTest 35: [ OK ] LifetimeModuleTest.BasicTest (0 ms) 35: [ RUN ] LifetimeModuleTest.CumulativeTest 35: [ OK ] LifetimeModuleTest.CumulativeTest (1 ms) 35: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets 35: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (0 ms) 35: [----------] 3 tests from LifetimeModuleTest (1 ms total) 35: 35: [----------] Global test environment tear-down 35: [==========] 69 tests from 14 test cases ran. (28 ms total) 35: [ PASSED ] 69 tests. 35/54 Test #35: AnalysisDataUnitTests ............... Passed 0.11 sec test 36 Start 36: CoordinateIOTests 36: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/coordinateio-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/CoordinateIOTests.xml" 36: Test timeout computed to be: 30 36: [==========] Running 64 tests from 19 test cases. 36: [----------] Global test environment set-up. 36: [----------] 1 test from OutputSelectorDeathTest 36: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (40 ms) 36: [----------] 1 test from OutputSelectorDeathTest (40 ms total) 36: 36: [----------] 5 tests from TrajectoryFrameWriterTest 36: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (5 ms) 36: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (5 ms) 36: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (3 ms) 36: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (5 ms) 36: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks 36: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (1 ms) 36: [----------] 5 tests from TrajectoryFrameWriterTest (19 ms total) 36: 36: [----------] 5 tests from OutputAdapterContainer 36: [ RUN ] OutputAdapterContainer.MakeEmpty 36: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms) 36: [ RUN ] OutputAdapterContainer.AddAdapter 36: [ OK ] OutputAdapterContainer.AddAdapter (0 ms) 36: [ RUN ] OutputAdapterContainer.RejectBadAdapter 36: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms) 36: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter 36: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms) 36: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters 36: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms) 36: [----------] 5 tests from OutputAdapterContainer (0 ms total) 36: 36: [----------] 5 tests from FlagTest 36: [ RUN ] FlagTest.CanSetSimpleFlag 36: [ OK ] FlagTest.CanSetSimpleFlag (0 ms) 36: [ RUN ] FlagTest.CanAddNewBox 36: [ OK ] FlagTest.CanAddNewBox (0 ms) 36: [ RUN ] FlagTest.SetsImplicitPrecisionChange 36: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms) 36: [ RUN ] FlagTest.SetsImplicitStartTimeChange 36: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms) 36: [ RUN ] FlagTest.SetsImplicitTimeStepChange 36: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms) 36: [----------] 5 tests from FlagTest (0 ms total) 36: 36: [----------] 5 tests from SetAtomsTest 36: [ RUN ] SetAtomsTest.RemovesExistingAtoms 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] SetAtomsTest.RemovesExistingAtoms (3 ms) 36: [ RUN ] SetAtomsTest.AddsNewAtoms 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] SetAtomsTest.AddsNewAtoms (2 ms) 36: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (3 ms) 36: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (3 ms) 36: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (3 ms) 36: [----------] 5 tests from SetAtomsTest (14 ms total) 36: 36: [----------] 2 tests from SetBothTimeTest 36: [ RUN ] SetBothTimeTest.StartTimeZeroWorks 36: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms) 36: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks 36: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms) 36: [----------] 2 tests from SetBothTimeTest (0 ms total) 36: 36: [----------] 2 tests from SetStartTimeTest 36: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart 36: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms) 36: [ RUN ] SetStartTimeTest.WorksWithZeroStart 36: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms) 36: [----------] 2 tests from SetStartTimeTest (0 ms total) 36: 36: [----------] 1 test from SetTimeStepTest 36: [ RUN ] SetTimeStepTest.SetTimeStepWorks 36: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms) 36: [----------] 1 test from SetTimeStepTest (0 ms total) 36: 36: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest 36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (2 ms) 36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (3 ms) 36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (3 ms) 36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (3 ms) 36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (3 ms) 36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (5 ms) 36: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (19 ms total) 36: 36: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles 36: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (4 ms) 36: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (5 ms) 36: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (5 ms) 36: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (14 ms total) 36: 36: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles 36: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 36: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms) 36: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 36: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms) 36: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 36: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms) 36: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total) 36: 36: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles 36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (6 ms) 36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (6 ms) 36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (6 ms) 36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (6 ms) 36: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (24 ms total) 36: 36: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles 36: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (3 ms) 36: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (2 ms) 36: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (3 ms) 36: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (8 ms total) 36: 36: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles 36: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 36: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms) 36: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 36: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms) 36: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 36: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms) 36: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (0 ms total) 36: 36: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles 36: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (3 ms) 36: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (3 ms) 36: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (6 ms total) 36: 36: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles 36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms) 36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms) 36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms) 36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms) 36: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (0 ms total) 36: 36: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles 36: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (3 ms) 36: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (2 ms) 36: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (5 ms total) 36: 36: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles 36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms) 36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms) 36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms) 36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (1 ms) 36: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (1 ms total) 36: 36: [----------] 4 tests from ModuleSupported/NoOptionalOutput 36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (2 ms) 36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (3 ms) 36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (3 ms) 36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3 36: 36: WARNING: Masses and atomic (Van der Waals) radii will be guessed 36: based on residue and atom names, since they could not be 36: definitively assigned from the information in your input 36: files. These guessed numbers might deviate from the mass 36: and radius of the atom type. Please check the output 36: files if necessary. 36: 36: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (4 ms) 36: [----------] 4 tests from ModuleSupported/NoOptionalOutput (12 ms total) 36: 36: [----------] Global test environment tear-down 36: [==========] 64 tests from 19 test cases ran. (162 ms total) 36: [ PASSED ] 64 tests. 36/54 Test #36: CoordinateIOTests ................... Passed 0.40 sec test 37 Start 37: TrajectoryAnalysisUnitTests 37: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/trajectoryanalysis-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" 37: Test timeout computed to be: 30 37: [==========] Running 82 tests from 16 test cases. 37: [----------] Global test environment set-up. 37: [----------] 5 tests from ClustsizeTest 37: [ RUN ] ClustsizeTest.NoMolDefaultCutoff 37: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 37: There is one group in the index 37: '', 24 atoms 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Total number of atoms in clusters = 24 37: cmid: 2, cmax: 4, max_size: 6 37: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 37: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (4 ms) 37: [ RUN ] ClustsizeTest.NoMolShortCutoff 37: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 37: There is one group in the index 37: '', 24 atoms 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Total number of atoms in clusters = 24 37: cmid: 1, cmax: 6, max_size: 6 37: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 37: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (3 ms) 37: [ RUN ] ClustsizeTest.MolDefaultCutoff 37: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: '', 24 atoms 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Total number of atoms in clusters = 8 37: cmid: 2, cmax: 4, max_size: 2 37: 50%100%cmid: 2, cmax: 6, max_size: 2 37: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (4 ms) 37: [ RUN ] ClustsizeTest.MolShortCutoff 37: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: '', 24 atoms 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Total number of atoms in clusters = 8 37: cmid: 1, cmax: 6, max_size: 2 37: 50%100%cmid: 2, cmax: 6, max_size: 2 37: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (4 ms) 37: [ RUN ] ClustsizeTest.MolCSize 37: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: '', 24 atoms 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Total number of atoms in clusters = 8 37: cmid: 2, cmax: 4, max_size: 2 37: 50%100%cmid: 2, cmax: 6, max_size: 2 37: 50%100%[ OK ] ClustsizeTest.MolCSize (4 ms) 37: [----------] 5 tests from ClustsizeTest (19 ms total) 37: 37: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest 37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp 37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (1 ms) 37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory 37: Reading frames from gro file 'Test system', 8 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (3 ms) 37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset 37: Reading frames from gro file 'Test system', 8 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (2 ms) 37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory 37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (1 ms) 37: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (7 ms total) 37: 37: [----------] 11 tests from AngleModuleTest 37: [ RUN ] AngleModuleTest.ComputesSimpleAngles 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.ComputesSimpleAngles (2 ms) 37: [ RUN ] AngleModuleTest.ComputesDihedrals 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.ComputesDihedrals (3 ms) 37: [ RUN ] AngleModuleTest.ComputesVectorPairAngles 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.ComputesVectorPairAngles (2 ms) 37: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (2 ms) 37: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (3 ms) 37: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (3 ms) 37: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles 37: Reading frames from gro file 'Test system for different angles', 33 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (3 ms) 37: [ RUN ] AngleModuleTest.ComputesMultipleAngles 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.ComputesMultipleAngles (4 ms) 37: [ RUN ] AngleModuleTest.HandlesDynamicSelections 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.HandlesDynamicSelections (3 ms) 37: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (4 ms) 37: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (4 ms) 37: [----------] 11 tests from AngleModuleTest (33 ms total) 37: 37: [----------] 4 tests from ConvertTrjModuleTest 37: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput 37: Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 37: Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: Analyzed 1 frames, last time 0.000 37: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (13 ms) 37: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset 37: Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 37: Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: Analyzed 1 frames, last time 0.000 37: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (12 ms) 37: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding 37: Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (3 ms) 37: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection 37: Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 37: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (2 ms) 37: [----------] 4 tests from ConvertTrjModuleTest (31 ms total) 37: 37: [----------] 3 tests from DistanceModuleTest 37: [ RUN ] DistanceModuleTest.ComputesDistances 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: atomname S1 S2: 37: Number of samples: 5 37: Average distance: 1.43246 nm 37: Standard deviation: 0.96700 nm 37: [ OK ] DistanceModuleTest.ComputesDistances (6 ms) 37: [ RUN ] DistanceModuleTest.ComputesMultipleDistances 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: atomname S1 S2: 37: Number of samples: 5 37: Average distance: 1.43246 nm 37: Standard deviation: 0.96700 nm 37: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: 37: Number of samples: 4 37: Average distance: 1.81066 nm 37: Standard deviation: 0.79289 nm 37: [ OK ] DistanceModuleTest.ComputesMultipleDistances (5 ms) 37: [ RUN ] DistanceModuleTest.HandlesDynamicSelections 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: atomname S1 S2 and res_cog x < 2.8: 37: Number of samples: 3 37: Average distance: 1.72076 nm 37: Standard deviation: 1.24839 nm 37: [ OK ] DistanceModuleTest.HandlesDynamicSelections (6 ms) 37: [----------] 3 tests from DistanceModuleTest (17 ms total) 37: 37: [----------] 2 tests from ExtractClusterModuleTest 37: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms 37: trr version: GMX_trn_file (single precision) 37: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 37: Analyzed 26 frames, last time 0.050 37: There are 8 clusters containing 26 structures, highest framenr is 25 37: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (4 ms) 37: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset 37: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 37: Analyzed 26 frames, last time 0.050 37: There are 8 clusters containing 26 structures, highest framenr is 25 37: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (2 ms) 37: [----------] 2 tests from ExtractClusterModuleTest (6 ms total) 37: 37: [----------] 2 tests from FreeVolumeModuleTest 37: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume 37: Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 37: Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 37: from the source below. This means the results may be different 37: compared to previous GROMACS versions. 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: A. Bondi 37: van der Waals Volumes and Radii 37: J. Phys. Chem. 68 (1964) pp. 441-451 37: -------- -------- --- Thank You --- -------- -------- 37: 37: Could not determine VDW radius for CO2-RM. Set to zero. 37: Could not determine VDW radius for CO2-RM. Set to zero. 37: Could not determine VDW radius for CO2-RM. Set to zero. 37: Could not determine VDW radius for CO2-RM. Set to zero. 37: Could not determine VDW radius for CO2-RM. Set to zero. 37: Could not determine VDW radius for CO2-RM. Set to zero. 37: Could not determine VDW radius for CO2-RM. Set to zero. 37: Could not determine VDW radius for CO2-RM. Set to zero. 37: Could not determine VDW radius for CO2-RM. Set to zero. 37: Could not determine VDW radius for 40 particles. These were set to zero. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: Analyzed 1 frames, last time 0.000 37: cutoff = 0.18 nm 37: probe_radius = 0 nm 37: seed = 13 37: ninsert = 1000 probes per nm^3 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: A. Bondi 37: van der Waals Volumes and Radii 37: J. Phys. Chem. 68 (1964) pp. 441-451 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David 37: van der Spoel and Luciano T. Costa 37: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 37: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 37: Environ. Sci. Technol. 47 (2013) pp. 7421-7429 37: -------- -------- --- Thank You --- -------- -------- 37: 37: Free volume 38.02 +/- 0.00 % 37: Total volume 68.92 +/- 0.00 nm^3 37: Number of molecules 340 total mass 63491.38 Dalton 37: Average molar mass: 186.74 Dalton 37: Density rho: 1529.71 +/- 0.00 nm^3 37: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 37: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 37: Fractional free volume 0.194 +/- 0.000 37: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (143 ms) 37: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection 37: Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 37: Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 37: from the source below. This means the results may be different 37: compared to previous GROMACS versions. 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: A. Bondi 37: van der Waals Volumes and Radii 37: J. Phys. Chem. 68 (1964) pp. 441-451 37: -------- -------- --- Thank You --- -------- -------- 37: 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: Analyzed 1 frames, last time 0.000 37: cutoff = 0.18 nm 37: probe_radius = 0 nm 37: seed = 17 37: ninsert = 1000 probes per nm^3 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: A. Bondi 37: van der Waals Volumes and Radii 37: J. Phys. Chem. 68 (1964) pp. 441-451 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David 37: van der Spoel and Luciano T. Costa 37: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 37: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 37: Environ. Sci. Technol. 47 (2013) pp. 7421-7429 37: -------- -------- --- Thank You --- -------- -------- 37: 37: Free volume 38.48 +/- 0.00 % 37: Total volume 68.92 +/- 0.00 nm^3 37: Number of molecules 340 total mass 63491.38 Dalton 37: Average molar mass: 186.74 Dalton 37: Density rho: 1529.71 +/- 0.00 nm^3 37: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 37: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 37: Fractional free volume 0.200 +/- 0.000 37: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (123 ms) 37: [----------] 2 tests from FreeVolumeModuleTest (266 ms total) 37: 37: [----------] 9 tests from PairDistanceModuleTest 37: [ RUN ] PairDistanceModuleTest.ComputesAllDistances 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] PairDistanceModuleTest.ComputesAllDistances (3 ms) 37: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (3 ms) 37: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (2 ms) 37: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (3 ms) 37: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (3 ms) 37: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (4 ms) 37: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (3 ms) 37: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (4 ms) 37: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (4 ms) 37: [----------] 9 tests from PairDistanceModuleTest (29 ms total) 37: 37: [----------] 5 tests from RdfModuleTest 37: [ RUN ] RdfModuleTest.BasicTest 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] RdfModuleTest.BasicTest (47 ms) 37: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork 37: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: Analyzed 1 frames, last time 0.000 37: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (21 ms) 37: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (31 ms) 37: [ RUN ] RdfModuleTest.CalculatesSurf 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] RdfModuleTest.CalculatesSurf (15 ms) 37: [ RUN ] RdfModuleTest.CalculatesXY 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] RdfModuleTest.CalculatesXY (54 ms) 37: [----------] 5 tests from RdfModuleTest (168 ms total) 37: 37: [----------] 5 tests from SasaModuleTest 37: [ RUN ] SasaModuleTest.BasicTest 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 37: Michael Scharf 37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 37: of Surface Area and Volume and to Dot Surface Contouring of Molecular 37: Assemblies 37: J. Comp. Chem. 16 (1995) pp. 273-284 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 37: from the source below. This means the results may be different 37: compared to previous GROMACS versions. 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: A. Bondi 37: van der Waals Volumes and Radii 37: J. Phys. Chem. 68 (1964) pp. 441-451 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: [ OK ] SasaModuleTest.BasicTest (18 ms) 37: [ RUN ] SasaModuleTest.HandlesSelectedResidues 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 37: Michael Scharf 37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 37: of Surface Area and Volume and to Dot Surface Contouring of Molecular 37: Assemblies 37: J. Comp. Chem. 16 (1995) pp. 273-284 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 37: from the source below. This means the results may be different 37: compared to previous GROMACS versions. 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: A. Bondi 37: van der Waals Volumes and Radii 37: J. Phys. Chem. 68 (1964) pp. 441-451 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: [ OK ] SasaModuleTest.HandlesSelectedResidues (7 ms) 37: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 37: Michael Scharf 37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 37: of Surface Area and Volume and to Dot Surface Contouring of Molecular 37: Assemblies 37: J. Comp. Chem. 16 (1995) pp. 273-284 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 37: from the source below. This means the results may be different 37: compared to previous GROMACS versions. 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: A. Bondi 37: van der Waals Volumes and Radii 37: J. Phys. Chem. 68 (1964) pp. 441-451 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (6 ms) 37: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 37: Michael Scharf 37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 37: of Surface Area and Volume and to Dot Surface Contouring of Molecular 37: Assemblies 37: J. Comp. Chem. 16 (1995) pp. 273-284 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 37: from the source below. This means the results may be different 37: compared to previous GROMACS versions. 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: A. Bondi 37: van der Waals Volumes and Radii 37: J. Phys. Chem. 68 (1964) pp. 441-451 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (8 ms) 37: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 37: Michael Scharf 37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 37: of Surface Area and Volume and to Dot Surface Contouring of Molecular 37: Assemblies 37: J. Comp. Chem. 16 (1995) pp. 273-284 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 37: from the source below. This means the results may be different 37: compared to previous GROMACS versions. 37: 37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 37: A. Bondi 37: van der Waals Volumes and Radii 37: J. Phys. Chem. 68 (1964) pp. 441-451 37: -------- -------- --- Thank You --- -------- -------- 37: 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (53 ms) 37: [----------] 5 tests from SasaModuleTest (94 ms total) 37: 37: [----------] 8 tests from SelectModuleTest 37: [ RUN ] SelectModuleTest.BasicTest 37: Reading frames from gro file 'Test system', 15 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] SelectModuleTest.BasicTest (7 ms) 37: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput 37: Reading frames from gro file 'Test system', 15 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (5 ms) 37: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput 37: Reading frames from gro file 'Test system', 15 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (6 ms) 37: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput 37: Reading frames from gro file 'Test system', 15 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (5 ms) 37: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput 37: Reading frames from gro file 'Test system', 15 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (5 ms) 37: [ RUN ] SelectModuleTest.NormalizesSizes 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] SelectModuleTest.NormalizesSizes (3 ms) 37: [ RUN ] SelectModuleTest.WritesResidueNumbers 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] SelectModuleTest.WritesResidueNumbers (4 ms) 37: [ RUN ] SelectModuleTest.WritesResidueIndices 37: 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Analyzed topology coordinates 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] SelectModuleTest.WritesResidueIndices (2 ms) 37: [----------] 8 tests from SelectModuleTest (37 ms total) 37: 37: [----------] 10 tests from SurfaceAreaTest 37: [ RUN ] SurfaceAreaTest.ComputesSinglePoint 37: [ OK ] SurfaceAreaTest.ComputesSinglePoint (1 ms) 37: [ RUN ] SurfaceAreaTest.ComputesTwoPoints 37: [ OK ] SurfaceAreaTest.ComputesTwoPoints (1 ms) 37: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius 37: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (1 ms) 37: [ RUN ] SurfaceAreaTest.SurfacePoints12 37: [ OK ] SurfaceAreaTest.SurfacePoints12 (0 ms) 37: [ RUN ] SurfaceAreaTest.SurfacePoints32 37: [ OK ] SurfaceAreaTest.SurfacePoints32 (0 ms) 37: [ RUN ] SurfaceAreaTest.SurfacePoints42 37: [ OK ] SurfaceAreaTest.SurfacePoints42 (0 ms) 37: [ RUN ] SurfaceAreaTest.SurfacePoints122 37: [ OK ] SurfaceAreaTest.SurfacePoints122 (56 ms) 37: [ RUN ] SurfaceAreaTest.Computes100Points 37: [ OK ] SurfaceAreaTest.Computes100Points (1 ms) 37: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC 37: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (3 ms) 37: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC 37: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (4 ms) 37: [----------] 10 tests from SurfaceAreaTest (67 ms total) 37: 37: [----------] 4 tests from TopologyInformation 37: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile 37: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms) 37: [ RUN ] TopologyInformation.WorksWithGroFile 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] TopologyInformation.WorksWithGroFile (4 ms) 37: [ RUN ] TopologyInformation.WorksWithPdbFile 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] TopologyInformation.WorksWithPdbFile (5 ms) 37: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile 37: 37: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to -411338305 37: Generated 330891 of the 330891 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 330891 of the 330891 1-4 parameter combinations 37: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 37: 37: NOTE 2 [file lysozyme.top, line 1465]: 37: System has non-zero total charge: 2.000000 37: Total charge should normally be an integer. See 37: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 37: for discussion on how close it should be to an integer. 37: 37: 37: 37: Number of degrees of freedom in T-Coupling group rest is 465.00 37: 37: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 37: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 37: Analysing residue names: 37: There are: 10 Protein residues 37: Analysing Protein... 37: This run will generate roughly 0 Mb of data 37: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (724 ms) 37: [----------] 4 tests from TopologyInformation (734 ms total) 37: 37: [----------] 4 tests from TrajectoryModuleTest 37: [ RUN ] TrajectoryModuleTest.BasicTest 37: Reading frames from gro file 'Test system', 15 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] TrajectoryModuleTest.BasicTest (43 ms) 37: [ RUN ] TrajectoryModuleTest.PlotsXOnly 37: Reading frames from gro file 'Test system', 15 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] TrajectoryModuleTest.PlotsXOnly (4 ms) 37: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities 37: Reading frames from gro file 'Test system', 15 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (4 ms) 37: [ RUN ] TrajectoryModuleTest.HandlesNoForces 37: Reading frames from gro file 'Test system', 15 atoms. 37: Reading frame 0 time 0.000 37: WARNING: If there are molecules in the input trajectory file 37: that are broken across periodic boundaries, they 37: cannot be made whole (or treated as whole) without 37: you providing a run input file. 37: 37: Reading frame 1 time 0.000 Last frame 1 time 0.000 37: Analyzed 2 frames, last time 0.000 37: 37: WARNING: Masses and atomic (Van der Waals) radii will be guessed 37: based on residue and atom names, since they could not be 37: definitively assigned from the information in your input 37: files. These guessed numbers might deviate from the mass 37: and radius of the atom type. Please check the output 37: files if necessary. 37: 37: [ OK ] TrajectoryModuleTest.HandlesNoForces (3 ms) 37: [----------] 4 tests from TrajectoryModuleTest (55 ms total) 37: 37: [----------] 5 tests from UnionFinderTest 37: [ RUN ] UnionFinderTest.WorksEmpty 37: [ OK ] UnionFinderTest.WorksEmpty (0 ms) 37: [ RUN ] UnionFinderTest.BasicMerges 37: [ OK ] UnionFinderTest.BasicMerges (1 ms) 37: [ RUN ] UnionFinderTest.LargerMerges 37: [ OK ] UnionFinderTest.LargerMerges (0 ms) 37: [ RUN ] UnionFinderTest.LongRightMerge 37: [ OK ] UnionFinderTest.LongRightMerge (0 ms) 37: [ RUN ] UnionFinderTest.LongLeftMerge 37: [ OK ] UnionFinderTest.LongLeftMerge (0 ms) 37: [----------] 5 tests from UnionFinderTest (1 ms total) 37: 37: [----------] 1 test from MappedUnionFinderTest 37: [ RUN ] MappedUnionFinderTest.BasicMerges 37: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) 37: [----------] 1 test from MappedUnionFinderTest (0 ms total) 37: 37: [----------] Global test environment tear-down 37: [==========] 82 tests from 16 test cases ran. (1564 ms total) 37: [ PASSED ] 82 tests. 37/54 Test #37: TrajectoryAnalysisUnitTests ......... Passed 1.59 sec test 38 Start 38: EnergyAnalysisUnitTests 38: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/energyanalysis-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/EnergyAnalysisUnitTests.xml" 38: Test timeout computed to be: 30 38: [==========] Running 7 tests from 4 test cases. 38: [----------] Global test environment set-up. 38: [----------] 1 test from DhdlTest 38: [ RUN ] DhdlTest.ExtractDhdl 38: Opened /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file 38: Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) 38: Note: file tpx version 110, software tpx version 119 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Reading energy frame 6 time 0.060 Reading energy frame 7 time 0.070 Reading energy frame 8 time 0.080 Reading energy frame 9 time 0.090 Reading energy frame 10 time 0.100 Reading energy frame 11 time 0.110 Reading energy frame 12 time 0.120 Reading energy frame 13 time 0.130 Reading energy frame 14 time 0.140 Reading energy frame 15 time 0.150 Reading energy frame 16 time 0.160 Reading energy frame 17 time 0.170 Reading energy frame 18 time 0.180 Reading energy frame 19 time 0.190 Reading energy frame 20 time 0.200 Reading energy frame 30 time 0.300 Reading energy frame 40 time 0.400 Reading energy frame 50 time 0.500 Reading energy frame 60 time 0.600 Reading energy frame 70 time 0.700 Reading energy frame 80 time 0.800 Reading energy frame 90 time 0.900 Reading energy frame 100 time 1.000 Last energy frame read 100 time 1.000 38: 38: 38: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg 38: [ OK ] DhdlTest.ExtractDhdl (77 ms) 38: [----------] 1 test from DhdlTest (78 ms total) 38: 38: [----------] 1 test from OriresTest 38: [ RUN ] OriresTest.ExtractOrires 38: Opened /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file 38: Reading file /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) 38: Note: file tpx version 111, software tpx version 119 38: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) 38: End your selection with 0 38: Selecting all 7 orientation restraints 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Reading energy frame 3 time 0.006 Reading energy frame 4 time 0.008 Reading energy frame 5 time 0.010 Reading energy frame 6 time 0.012 Reading energy frame 7 time 0.014 Reading energy frame 8 time 0.016 Reading energy frame 9 time 0.018 Reading energy frame 10 time 0.020 Last energy frame read 10 time 0.020 38: [ OK ] OriresTest.ExtractOrires (319 ms) 38: [----------] 1 test from OriresTest (320 ms total) 38: 38: [----------] 3 tests from EnergyTest 38: [ RUN ] EnergyTest.ExtractEnergy 38: Opened /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 38: 38: Select the terms you want from the following list by 38: selecting either (part of) the name or the number or a combination. 38: End your selection with an empty line or a zero. 38: ------------------------------------------------------------------- 38: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 38: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 38: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 38: 13 Box-Z 14 Volume 15 Density 16 pV 38: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 38: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 38: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 38: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 38: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 38: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 38: 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 38: 38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 38: All statistics are over 5001 points 38: 38: Energy Average Err.Est. RMSD Tot-Drift 38: ------------------------------------------------------------------------------- 38: Potential -34142.2 39 228.993 -62.8906 (kJ/mol) 38: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 38: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 38: [ OK ] EnergyTest.ExtractEnergy (3 ms) 38: [ RUN ] EnergyTest.ExtractEnergyByNumber 38: Opened /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 38: 38: Select the terms you want from the following list by 38: selecting either (part of) the name or the number or a combination. 38: End your selection with an empty line or a zero. 38: ------------------------------------------------------------------- 38: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 38: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 38: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 38: 13 Box-Z 14 Volume 15 Density 16 pV 38: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 38: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 38: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 38: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 38: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 38: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 38: 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 38: 38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 38: All statistics are over 5001 points 38: 38: Energy Average Err.Est. RMSD Tot-Drift 38: ------------------------------------------------------------------------------- 38: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) 38: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 38: Pres. DC -268.49 3 8.52175 13.2804 (bar) 38: [ OK ] EnergyTest.ExtractEnergyByNumber (4 ms) 38: [ RUN ] EnergyTest.ExtractEnergyMixed 38: Opened /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 38: 38: Select the terms you want from the following list by 38: selecting either (part of) the name or the number or a combination. 38: End your selection with an empty line or a zero. 38: ------------------------------------------------------------------- 38: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 38: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 38: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 38: 13 Box-Z 14 Volume 15 Density 16 pV 38: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 38: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 38: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 38: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 38: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 38: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 38: 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 38: 38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets 38: All statistics are over 5001 points 38: 38: Energy Average Err.Est. RMSD Tot-Drift 38: ------------------------------------------------------------------------------- 38: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 38: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 38: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) 38: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 38: [ OK ] EnergyTest.ExtractEnergyMixed (4 ms) 38: [----------] 3 tests from EnergyTest (11 ms total) 38: 38: [----------] 2 tests from ViscosityTest 38: [ RUN ] ViscosityTest.EinsteinViscosity 38: Opened /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 38: 38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 38: All statistics are over 5001 points 38: 38: Energy Average Err.Est. RMSD Tot-Drift 38: ------------------------------------------------------------------------------- 38: Pres-XX 20.2092 65 717.193 185.978 (bar) 38: Pres-XY -47.7351 39 372.522 207.456 (bar) 38: Pres-XZ 11.477 31 379.79 6.80818 (bar) 38: Pres-YX -47.7106 39 372.525 207.5 (bar) 38: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 38: Pres-YZ -41.3534 45 401.216 114.663 (bar) 38: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 38: Pres-ZY -41.3119 45 401.196 114.743 (bar) 38: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 38: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 38: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 38: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 38: [ OK ] ViscosityTest.EinsteinViscosity (767 ms) 38: [ RUN ] ViscosityTest.EinsteinViscosityIntegral 38: Opened /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 38: 38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 38: All statistics are over 5001 points 38: 38: Energy Average Err.Est. RMSD Tot-Drift 38: ------------------------------------------------------------------------------- 38: Pres-XX 20.2092 65 717.193 185.978 (bar) 38: Pres-XY -47.7351 39 372.522 207.456 (bar) 38: Pres-XZ 11.477 31 379.79 6.80818 (bar) 38: Pres-YX -47.7106 39 372.525 207.5 (bar) 38: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 38: Pres-YZ -41.3534 45 401.216 114.663 (bar) 38: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 38: Pres-ZY -41.3119 45 401.196 114.743 (bar) 38: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 38: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 38: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 38: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 38: [ OK ] ViscosityTest.EinsteinViscosityIntegral (1096 ms) 38: [----------] 2 tests from ViscosityTest (1863 ms total) 38: 38: [----------] Global test environment tear-down 38: [==========] 7 tests from 4 test cases ran. (2273 ms total) 38: [ PASSED ] 7 tests. 38/54 Test #38: EnergyAnalysisUnitTests ............. Passed 2.30 sec test 39 Start 39: ToolUnitTests 39: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/tool-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/ToolUnitTests.xml" 39: Test timeout computed to be: 30 39: [==========] Running 18 tests from 4 test cases. 39: [----------] Global test environment set-up. 39: [----------] 2 tests from DumpTest 39: 39: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 39: For a correct single-point energy evaluation with nsteps = 0, use 39: continuation = yes to avoid constraining the input coordinates. 39: 39: Setting the LD random seed to -1084231746 39: Generated 330891 of the 330891 non-bonded parameter combinations 39: Generating 1-4 interactions: fudge = 0.5 39: Generated 330891 of the 330891 1-4 parameter combinations 39: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 39: 39: NOTE 2 [file lysozyme.top, line 1465]: 39: System has non-zero total charge: 2.000000 39: Total charge should normally be an integer. See 39: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 39: for discussion on how close it should be to an integer. 39: 39: 39: 39: Number of degrees of freedom in T-Coupling group rest is 465.00 39: 39: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 39: NVE simulation with an initial temperature of zero: will use a Verlet 39: buffer of 10%. Check your energy drift! 39: 39: 39: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 39: You are using a plain Coulomb cut-off, which might produce artifacts. 39: You might want to consider using PME electrostatics. 39: 39: 39: 39: There were 4 notes 39: Analysing residue names: 39: There are: 10 Protein residues 39: Analysing Protein... 39: This run will generate roughly 0 Mb of data 39: [ RUN ] DumpTest.WorksWithTpr 39: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 39: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 39: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr: 39: inputrec: 39: integrator = md 39: tinit = 0 39: dt = 0.001 39: nsteps = 0 39: init-step = 0 39: simulation-part = 1 39: comm-mode = Linear 39: nstcomm = 100 39: bd-fric = 0 39: ld-seed = -1084231746 39: emtol = 10 39: emstep = 0.01 39: niter = 20 39: fcstep = 0 39: nstcgsteep = 1000 39: nbfgscorr = 10 39: rtpi = 0.05 39: nstxout = 0 39: nstvout = 0 39: nstfout = 0 39: nstlog = 1000 39: nstcalcenergy = 100 39: nstenergy = 1000 39: nstxout-compressed = 0 39: compressed-x-precision = 1000 39: cutoff-scheme = Verlet 39: nstlist = 10 39: pbc = xyz 39: periodic-molecules = false 39: verlet-buffer-tolerance = -1 39: rlist = 1.1 39: coulombtype = Cut-off 39: coulomb-modifier = Potential-shift 39: rcoulomb-switch = 0 39: rcoulomb = 1 39: epsilon-r = 1 39: epsilon-rf = inf 39: vdw-type = Cut-off 39: vdw-modifier = Potential-shift 39: rvdw-switch = 0 39: rvdw = 1 39: DispCorr = No 39: table-extension = 1 39: fourierspacing = 0.12 39: fourier-nx = 0 39: fourier-ny = 0 39: fourier-nz = 0 39: pme-order = 4 39: ewald-rtol = 1e-05 39: ewald-rtol-lj = 0.001 39: lj-pme-comb-rule = Geometric 39: ewald-geometry = 0 39: epsilon-surface = 0 39: tcoupl = No 39: nsttcouple = -1 39: nh-chain-length = 0 39: print-nose-hoover-chain-variables = false 39: pcoupl = No 39: pcoupltype = Isotropic 39: nstpcouple = -1 39: tau-p = 1 39: compressibility (3x3): 39: compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: ref-p (3x3): 39: ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: refcoord-scaling = No 39: posres-com (3): 39: posres-com[0]= 0.00000e+00 39: posres-com[1]= 0.00000e+00 39: posres-com[2]= 0.00000e+00 39: posres-comB (3): 39: posres-comB[0]= 0.00000e+00 39: posres-comB[1]= 0.00000e+00 39: posres-comB[2]= 0.00000e+00 39: QMMM = false 39: QMconstraints = 0 39: QMMMscheme = 0 39: MMChargeScaleFactor = 1 39: qm-opts: 39: ngQM = 0 39: constraint-algorithm = Lincs 39: continuation = false 39: Shake-SOR = false 39: shake-tol = 0.0001 39: lincs-order = 4 39: lincs-iter = 1 39: lincs-warnangle = 30 39: nwall = 0 39: wall-type = 9-3 39: wall-r-linpot = -1 39: wall-atomtype[0] = -1 39: wall-atomtype[1] = -1 39: wall-density[0] = 0 39: wall-density[1] = 0 39: wall-ewald-zfac = 3 39: pull = false 39: awh = false 39: rotation = false 39: interactiveMD = false 39: disre = No 39: disre-weighting = Conservative 39: disre-mixed = false 39: dr-fc = 1000 39: dr-tau = 0 39: nstdisreout = 100 39: orire-fc = 0 39: orire-tau = 0 39: nstorireout = 100 39: free-energy = no 39: cos-acceleration = 0 39: deform (3x3): 39: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: simulated-tempering = false 39: swapcoords = no 39: userint1 = 0 39: userint2 = 0 39: userint3 = 0 39: userint4 = 0 39: userreal1 = 0 39: userreal2 = 0 39: userreal3 = 0 39: userreal4 = 0 39: applied-forces: 39: electric-field: 39: x: 39: E0 = 0 39: omega = 0 39: t0 = 0 39: sigma = 0 39: y: 39: E0 = 0 39: omega = 0 39: t0 = 0 39: sigma = 0 39: z: 39: E0 = 0 39: omega = 0 39: t0 = 0 39: sigma = 0 39: density-guided-simulation: 39: active = false 39: group = protein 39: similarity-measure = inner-product 39: atom-spreading-weight = unity 39: force-constant = 1e+09 39: gaussian-transform-spreading-width = 0.2 39: gaussian-transform-spreading-range-in-multiples-of-width = 4 39: reference-density-filename = reference.mrc 39: nst = 1 39: normalize-densities = true 39: adaptive-force-scaling = false 39: adaptive-force-scaling-time-constant = 4 39: grpopts: 39: nrdf: 465 39: ref-t: 0 39: tau-t: 0 39: annealing: No 39: annealing-npoints: 0 39: acc: 0 0 0 39: nfreeze: N N N 39: energygrp-flags[ 0]: 0 39: header: 39: bIr = present 39: bBox = present 39: bTop = present 39: bX = present 39: bV = present 39: bF = not present 39: natoms = 156 39: lambda = 0.000000e+00 39: buffer size = 70122 39: topology: 39: name="First 10 residues from 1AKI" 39: #atoms = 156 39: #molblock = 1 39: molblock (0): 39: moltype = 0 "Protein_chain_B" 39: #molecules = 1 39: #posres_xA = 0 39: #posres_xB = 0 39: bIntermolecularInteractions = false 39: ffparams: 39: atnr=10 39: ntypes=212 39: functype[0]=LJ_SR, c6= 3.35274678e-03, c12= 3.95094442e-06 39: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[2]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06 39: functype[3]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07 39: functype[4]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06 39: functype[5]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06 39: functype[6]=LJ_SR, c6= 2.80388560e-03, c12= 4.30621225e-06 39: functype[7]=LJ_SR, c6= 5.81477529e-04, c12= 2.82897505e-07 39: functype[8]=LJ_SR, c6= 6.03335344e-04, c12= 2.35915461e-07 39: functype[9]=LJ_SR, c6= 7.20490366e-03, c12= 1.15394674e-05 39: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[20]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06 39: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[22]=LJ_SR, c6= 2.03050409e-03, c12= 3.73260587e-06 39: functype[23]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07 39: functype[24]=LJ_SR, c6= 3.15004110e-03, c12= 7.12219987e-06 39: functype[25]=LJ_SR, c6= 2.19084952e-03, c12= 2.43608151e-06 39: functype[26]=LJ_SR, c6= 2.18203568e-03, c12= 4.18553559e-06 39: functype[27]=LJ_SR, c6= 4.52516577e-04, c12= 2.74969627e-07 39: functype[28]=LJ_SR, c6= 4.69526733e-04, c12= 2.29304201e-07 39: functype[29]=LJ_SR, c6= 5.60698940e-03, c12= 1.12160870e-05 39: functype[30]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07 39: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[32]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07 39: functype[33]=LJ_SR, c6= 1.22578125e-04, c12= 2.99263000e-08 39: functype[34]=LJ_SR, c6= 7.73964023e-04, c12= 6.37726703e-07 39: functype[35]=LJ_SR, c6= 5.38290978e-04, c12= 2.18128423e-07 39: functype[36]=LJ_SR, c6= 5.36125420e-04, c12= 3.74775753e-07 39: functype[37]=LJ_SR, c6= 1.11183168e-04, c12= 2.46209706e-08 39: functype[38]=LJ_SR, c6= 1.15362558e-04, c12= 2.05320568e-08 39: functype[39]=LJ_SR, c6= 1.37763538e-03, c12= 1.00429619e-06 39: functype[40]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06 39: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[42]=LJ_SR, c6= 3.15004110e-03, c12= 7.12219987e-06 39: functype[43]=LJ_SR, c6= 7.73964023e-04, c12= 6.37726703e-07 39: functype[44]=LJ_SR, c6= 4.88684509e-03, c12= 1.35898974e-05 39: functype[45]=LJ_SR, c6= 3.39879445e-03, c12= 4.64829665e-06 39: functype[46]=LJ_SR, c6= 3.38512102e-03, c12= 7.98643684e-06 39: functype[47]=LJ_SR, c6= 7.02015733e-04, c12= 5.24670621e-07 39: functype[48]=LJ_SR, c6= 7.28404594e-04, c12= 4.37536244e-07 39: functype[49]=LJ_SR, c6= 8.69845432e-03, c12= 2.14014596e-05 39: functype[50]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06 39: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[52]=LJ_SR, c6= 2.19084952e-03, c12= 2.43608151e-06 39: functype[53]=LJ_SR, c6= 5.38290978e-04, c12= 2.18128423e-07 39: functype[54]=LJ_SR, c6= 3.39879445e-03, c12= 4.64829665e-06 39: functype[55]=LJ_SR, c6= 2.36385715e-03, c12= 1.58990617e-06 39: functype[56]=LJ_SR, c6= 2.35434729e-03, c12= 2.73168564e-06 39: functype[57]=LJ_SR, c6= 4.88251036e-04, c12= 1.79458653e-07 39: functype[58]=LJ_SR, c6= 5.06604455e-04, c12= 1.49655159e-07 39: functype[59]=LJ_SR, c6= 6.04976375e-03, c12= 7.32016804e-06 39: functype[60]=LJ_SR, c6= 2.80388560e-03, c12= 4.30621225e-06 39: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[62]=LJ_SR, c6= 2.18203568e-03, c12= 4.18553559e-06 39: functype[63]=LJ_SR, c6= 5.36125420e-04, c12= 3.74775753e-07 39: functype[64]=LJ_SR, c6= 3.38512102e-03, c12= 7.98643684e-06 39: functype[65]=LJ_SR, c6= 2.35434729e-03, c12= 2.73168564e-06 39: functype[66]=LJ_SR, c6= 2.34487570e-03, c12= 4.69342567e-06 39: functype[67]=LJ_SR, c6= 4.86286790e-04, c12= 3.08335570e-07 39: functype[68]=LJ_SR, c6= 5.04566372e-04, c12= 2.57128914e-07 39: functype[69]=LJ_SR, c6= 6.02542540e-03, c12= 1.25770931e-05 39: functype[70]=LJ_SR, c6= 5.81477529e-04, c12= 2.82897505e-07 39: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[72]=LJ_SR, c6= 4.52516577e-04, c12= 2.74969627e-07 39: functype[73]=LJ_SR, c6= 1.11183168e-04, c12= 2.46209706e-08 39: functype[74]=LJ_SR, c6= 7.02015733e-04, c12= 5.24670621e-07 39: functype[75]=LJ_SR, c6= 4.88251036e-04, c12= 1.79458653e-07 39: functype[76]=LJ_SR, c6= 4.86286790e-04, c12= 3.08335570e-07 39: functype[77]=LJ_SR, c6= 1.00847496e-04, c12= 2.02561691e-08 39: functype[78]=LJ_SR, c6= 1.04638366e-04, c12= 1.68921372e-08 39: functype[79]=LJ_SR, c6= 1.24956934e-03, c12= 8.26254733e-07 39: functype[80]=LJ_SR, c6= 6.03335344e-04, c12= 2.35915461e-07 39: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[82]=LJ_SR, c6= 4.69526733e-04, c12= 2.29304201e-07 39: functype[83]=LJ_SR, c6= 1.15362558e-04, c12= 2.05320568e-08 39: functype[84]=LJ_SR, c6= 7.28404594e-04, c12= 4.37536244e-07 39: functype[85]=LJ_SR, c6= 5.06604455e-04, c12= 1.49655159e-07 39: functype[86]=LJ_SR, c6= 5.04566372e-04, c12= 2.57128914e-07 39: functype[87]=LJ_SR, c6= 1.04638366e-04, c12= 1.68921372e-08 39: functype[88]=LJ_SR, c6= 1.08571736e-04, c12= 1.40867851e-08 39: functype[89]=LJ_SR, c6= 1.29654081e-03, c12= 6.89034944e-07 39: functype[90]=LJ_SR, c6= 7.20490366e-03, c12= 1.15394674e-05 39: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 39: functype[92]=LJ_SR, c6= 5.60698940e-03, c12= 1.12160870e-05 39: functype[93]=LJ_SR, c6= 1.37763538e-03, c12= 1.00429619e-06 39: functype[94]=LJ_SR, c6= 8.69845432e-03, c12= 2.14014596e-05 39: functype[95]=LJ_SR, c6= 6.04976375e-03, c12= 7.32016804e-06 39: functype[96]=LJ_SR, c6= 6.02542540e-03, c12= 1.25770931e-05 39: functype[97]=LJ_SR, c6= 1.24956934e-03, c12= 8.26254733e-07 39: functype[98]=LJ_SR, c6= 1.29654081e-03, c12= 6.89034944e-07 39: functype[99]=LJ_SR, c6= 1.54830174e-02, c12= 3.37031588e-05 39: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05 39: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05 39: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05 39: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05 39: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05 39: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05 39: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05 39: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05 39: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05 39: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05 39: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05 39: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05 39: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05 39: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05 39: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05 39: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05 39: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02 39: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02 39: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02 39: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02 39: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02 39: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02 39: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02 39: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02 39: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02 39: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02 39: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02 39: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02 39: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 39: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02 39: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02 39: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02 39: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02 39: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02 39: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02 39: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02 39: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02 39: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02 39: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02 39: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02 39: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39320000e+01, phiB= 1.80000000e+02, cpB= 4.39320000e+01, mult=2 39: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400000e+00, phiB= 1.80000000e+02, cpB= 4.18400000e+00, mult=2 39: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60240000e+00, phiB= 1.80000000e+02, cpB= 4.60240000e+00, mult=2 39: functype[143]=RBDIHS, rbcA[0]= 5.46010000e-01, rbcA[1]= 1.63803000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 5.46010000e-01, rbcB[1]= 1.63803000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[144]=RBDIHS, rbcA[0]= 7.25920000e-01, rbcA[1]= 2.17777000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 7.25920000e-01, rbcB[1]= 2.17777000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[145]=RBDIHS, rbcA[0]= 1.27612000e+00, rbcA[1]= 1.16734000e+00, rbcA[2]= 8.95380000e-01, rbcA[3]=-3.33884000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 1.27612000e+00, rbcB[1]= 1.16734000e+00, rbcB[2]= 8.95380000e-01, rbcB[3]=-3.33884000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[146]=RBDIHS, rbcA[0]=-6.91824000e+00, rbcA[1]= 4.67562000e+00, rbcA[2]= 2.24262000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-6.91824000e+00, rbcB[1]= 4.67562000e+00, rbcB[2]= 2.24262000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[147]=RBDIHS, rbcA[0]= 9.70690000e-01, rbcA[1]= 2.91206000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 9.70690000e-01, rbcB[1]= 2.91206000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[148]=RBDIHS, rbcA[0]= 6.27600000e-01, rbcA[1]= 1.88280000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 6.27600000e-01, rbcB[1]= 1.88280000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[149]=RBDIHS, rbcA[0]=-1.58990000e-01, rbcA[1]=-4.76980000e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35960000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-1.58990000e-01, rbcB[1]=-4.76980000e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35960000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654000e+00, rbcA[2]=-1.04934700e+01, rbcA[3]= 6.73624000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654000e+00, rbcB[2]=-1.04934700e+01, rbcB[3]= 6.73624000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[151]=RBDIHS, rbcA[0]= 5.00825000e+00, rbcA[1]=-1.69870000e+00, rbcA[2]=-3.72380000e-01, rbcA[3]=-2.93716000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 5.00825000e+00, rbcB[1]=-1.69870000e+00, rbcB[2]=-3.72380000e-01, rbcB[3]=-2.93716000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[152]=RBDIHS, rbcA[0]= 2.92880000e+00, rbcA[1]=-1.46440000e+00, rbcA[2]= 2.09200000e-01, rbcA[3]=-1.67360000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 2.92880000e+00, rbcB[1]=-1.46440000e+00, rbcB[2]= 2.09200000e-01, rbcB[3]=-1.67360000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[153]=RBDIHS, rbcA[0]= 5.77183000e+00, rbcA[1]=-2.67148000e+00, rbcA[2]= 9.58140000e-01, rbcA[3]=-4.05848000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 5.77183000e+00, rbcB[1]=-2.67148000e+00, rbcB[2]= 9.58140000e-01, rbcB[3]=-4.05848000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[154]=RBDIHS, rbcA[0]= 8.03330000e-01, rbcA[1]= 2.40999000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 8.03330000e-01, rbcB[1]= 2.40999000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[155]=RBDIHS, rbcA[0]= 2.05016000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 2.05016000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[156]=RBDIHS, rbcA[0]= 3.02879800e+01, rbcA[1]=-4.81160000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 3.02879800e+01, rbcB[1]=-4.81160000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[157]=RBDIHS, rbcA[0]= 2.54763800e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 2.54763800e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[158]=RBDIHS, rbcA[0]= 1.57025500e+01, rbcA[1]= 3.17565600e+01, rbcA[2]=-3.66936000e+00, rbcA[3]=-4.37897500e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 1.57025500e+01, rbcB[1]= 3.17565600e+01, rbcB[2]=-3.66936000e+00, rbcB[3]=-4.37897500e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[159]=RBDIHS, rbcA[0]=-1.03574900e+01, rbcA[1]=-2.95871600e+01, rbcA[2]=-1.16734000e+00, rbcA[3]= 4.11119900e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-1.03574900e+01, rbcB[1]=-2.95871600e+01, rbcB[2]=-1.16734000e+00, rbcB[3]= 4.11119900e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[160]=RBDIHS, rbcA[0]= 4.50199000e+00, rbcA[1]= 7.82410000e-01, rbcA[2]=-1.60247000e+00, rbcA[3]=-3.68192000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 4.50199000e+00, rbcB[1]= 7.82410000e-01, rbcB[2]=-1.60247000e+00, rbcB[3]=-3.68192000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[161]=RBDIHS, rbcA[0]= 4.22590000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]=-3.12964000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 4.22590000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]=-3.12964000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[162]=RBDIHS, rbcA[0]=-7.65670000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]= 4.02501000e+00, rbcA[3]=-5.96639000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-7.65670000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]= 4.02501000e+00, rbcB[3]=-5.96639000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[163]=RBDIHS, rbcA[0]= 9.66500000e-01, rbcA[1]= 2.89951000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86601000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 9.66500000e-01, rbcB[1]= 2.89951000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86601000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[164]=RBDIHS, rbcA[0]=-4.23421000e+00, rbcA[1]= 7.22159000e+00, rbcA[2]= 1.90790000e+00, rbcA[3]=-4.89528000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-4.23421000e+00, rbcB[1]= 7.22159000e+00, rbcB[2]= 1.90790000e+00, rbcB[3]=-4.89528000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[165]=RBDIHS, rbcA[0]= 3.03340000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03340000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 3.03340000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03340000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[166]=RBDIHS, rbcA[0]= 1.02319700e+01, rbcA[1]= 3.52083000e+00, rbcA[2]=-3.97899000e+00, rbcA[3]=-9.77382000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 1.02319700e+01, rbcB[1]= 3.52083000e+00, rbcB[2]=-3.97899000e+00, rbcB[3]=-9.77382000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[167]=RBDIHS, rbcA[0]= 5.49778000e+00, rbcA[1]= 1.41838000e+00, rbcA[2]=-6.91615000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 5.49778000e+00, rbcB[1]= 1.41838000e+00, rbcB[2]=-6.91615000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[168]=RBDIHS, rbcA[0]=-1.21755000e+00, rbcA[1]=-3.65264000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-1.21755000e+00, rbcB[1]=-3.65264000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[169]=RBDIHS, rbcA[0]=-1.26775000e+00, rbcA[1]= 3.02085000e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49782000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-1.26775000e+00, rbcB[1]= 3.02085000e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49782000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[170]=RBDIHS, rbcA[0]= 3.80117000e+00, rbcA[1]=-6.95172000e+00, rbcA[2]=-1.01671000e+00, rbcA[3]= 4.16726000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 3.80117000e+00, rbcB[1]=-6.95172000e+00, rbcB[2]=-1.01671000e+00, rbcB[3]= 4.16726000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[171]=RBDIHS, rbcA[0]= 3.70280000e-01, rbcA[1]= 1.11086000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 3.70280000e-01, rbcB[1]= 1.11086000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[172]=RBDIHS, rbcA[0]= 3.32042200e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042200e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 3.32042200e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042200e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[173]=RBDIHS, rbcA[0]= 1.63176000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 1.63176000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[174]=RBDIHS, rbcA[0]= 3.40787000e+00, rbcA[1]=-2.80537000e+00, rbcA[2]=-3.59820000e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 3.40787000e+00, rbcB[1]=-2.80537000e+00, rbcB[2]=-3.59820000e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[175]=RBDIHS, rbcA[0]=-1.62590200e+01, rbcA[1]= 9.08765000e+00, rbcA[2]= 7.17138000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-1.62590200e+01, rbcB[1]= 9.08765000e+00, rbcB[2]= 7.17138000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[176]=RBDIHS, rbcA[0]= 9.45590000e-01, rbcA[1]= 2.83675000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 9.45590000e-01, rbcB[1]= 2.83675000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[177]=RBDIHS, rbcA[0]=-1.50624000e+00, rbcA[1]= 5.37225000e+00, rbcA[2]= 1.17989000e+00, rbcA[3]=-5.04590000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-1.50624000e+00, rbcB[1]= 5.37225000e+00, rbcB[2]= 1.17989000e+00, rbcB[3]=-5.04590000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[178]=RBDIHS, rbcA[0]= 1.00416000e+00, rbcA[1]= 3.01248000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 1.00416000e+00, rbcB[1]= 3.01248000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[179]=RBDIHS, rbcA[0]= 8.79268000e+00, rbcA[1]=-1.18344400e+01, rbcA[2]= 1.07529000e+00, rbcA[3]= 1.96648000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 8.79268000e+00, rbcB[1]=-1.18344400e+01, rbcB[2]= 1.07529000e+00, rbcB[3]= 1.96648000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[180]=RBDIHS, rbcA[0]=-5.77392000e+00, rbcA[1]= 3.38485000e+00, rbcA[2]= 2.38906000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-5.77392000e+00, rbcB[1]= 3.38485000e+00, rbcB[2]= 2.38906000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[181]=RBDIHS, rbcA[0]=-9.08346000e+00, rbcA[1]= 9.75709000e+00, rbcA[2]= 3.45180000e+00, rbcA[3]=-4.12542000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-9.08346000e+00, rbcB[1]= 9.75709000e+00, rbcB[2]= 3.45180000e+00, rbcB[3]=-4.12542000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[182]=RBDIHS, rbcA[0]=-4.70700000e-01, rbcA[1]=-1.41210000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88280000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-4.70700000e-01, rbcB[1]=-1.41210000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88280000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[183]=RBDIHS, rbcA[0]= 3.43088000e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 3.43088000e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[184]=RBDIHS, rbcA[0]= 2.57316000e+00, rbcA[1]= 3.49782000e+00, rbcA[2]=-1.10039000e+00, rbcA[3]=-4.97059000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]= 2.57316000e+00, rbcB[1]= 3.49782000e+00, rbcB[2]=-1.10039000e+00, rbcB[3]=-4.97059000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[185]=RBDIHS, rbcA[0]=-8.22160000e-01, rbcA[1]= 1.12759000e+00, rbcA[2]=-3.05440000e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 39: rbcB[0]=-8.22160000e-01, rbcB[1]= 1.12759000e+00, rbcB[2]=-3.05440000e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 39: functype[186]=LJ14, c6A= 3.20536041e-04, c12A= 1.71928145e-07, c6B= 3.20536041e-04, c12B= 1.71928145e-07 39: functype[187]=LJ14, c6A= 1.30458481e-03, c12A= 1.92011187e-06, c6B= 1.30458481e-03, c12B= 1.92011187e-06 39: functype[188]=LJ14, c6A= 1.40760563e-03, c12A= 1.25315910e-06, c6B= 1.40760563e-03, c12B= 1.25315910e-06 39: functype[189]=LJ14, c6A= 1.67637339e-03, c12A= 1.97547221e-06, c6B= 1.67637339e-03, c12B= 1.97547221e-06 39: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00 39: functype[191]=LJ14, c6A= 2.49447081e-04, c12A= 1.67110056e-07, c6B= 2.49447081e-04, c12B= 1.67110056e-07 39: functype[192]=LJ14, c6A= 1.01525205e-03, c12A= 1.86630294e-06, c6B= 1.01525205e-03, c12B= 1.86630294e-06 39: functype[193]=LJ14, c6A= 6.12890625e-05, c12A= 1.49631500e-08, c6B= 6.12890625e-05, c12B= 1.49631500e-08 39: functype[194]=LJ14, c6A= 2.69145489e-04, c12A= 1.09064212e-07, c6B= 2.69145489e-04, c12B= 1.09064212e-07 39: functype[195]=LJ14, c6A= 1.09542476e-03, c12A= 1.21804075e-06, c6B= 1.09542476e-03, c12B= 1.21804075e-06 39: functype[196]=LJ14, c6A= 3.86982011e-04, c12A= 3.18863352e-07, c6B= 3.86982011e-04, c12B= 3.18863352e-07 39: functype[197]=LJ14, c6A= 1.57502055e-03, c12A= 3.56109993e-06, c6B= 1.57502055e-03, c12B= 3.56109993e-06 39: functype[198]=LJ14, c6A= 2.44342255e-03, c12A= 6.79494872e-06, c6B= 2.44342255e-03, c12B= 6.79494872e-06 39: functype[199]=LJ14, c6A= 1.40194280e-03, c12A= 2.15310613e-06, c6B= 1.40194280e-03, c12B= 2.15310613e-06 39: functype[200]=LJ14, c6A= 1.09101784e-03, c12A= 2.09276780e-06, c6B= 1.09101784e-03, c12B= 2.09276780e-06 39: functype[201]=LJ14, c6A= 2.68062710e-04, c12A= 1.87387876e-07, c6B= 2.68062710e-04, c12B= 1.87387876e-07 39: functype[202]=LJ14, c6A= 2.26258289e-04, c12A= 1.37484813e-07, c6B= 2.26258289e-04, c12B= 1.37484813e-07 39: functype[203]=LJ14, c6A= 2.43143395e-04, c12A= 1.54167785e-07, c6B= 2.43143395e-04, c12B= 1.54167785e-07 39: functype[204]=LJ14, c6A= 1.17243785e-03, c12A= 2.34671283e-06, c6B= 1.17243785e-03, c12B= 2.34671283e-06 39: functype[205]=LJ14, c6A= 1.69256051e-03, c12A= 3.99321842e-06, c6B= 1.69256051e-03, c12B= 3.99321842e-06 39: functype[206]=LJ14, c6A= 5.04237478e-05, c12A= 1.01280845e-08, c6B= 5.04237478e-05, c12B= 1.01280845e-08 39: functype[207]=LJ14, c6A= 2.34763367e-04, c12A= 1.14652101e-07, c6B= 2.34763367e-04, c12B= 1.14652101e-07 39: functype[208]=LJ14, c6A= 5.76812790e-05, c12A= 1.02660284e-08, c6B= 5.76812790e-05, c12B= 1.02660284e-08 39: functype[209]=LJ14, c6A= 3.60245183e-03, c12A= 5.76973368e-06, c6B= 3.60245183e-03, c12B= 5.76973368e-06 39: functype[210]=LJ14, c6A= 6.88817690e-04, c12A= 5.02148096e-07, c6B= 6.88817690e-04, c12B= 5.02148096e-07 39: functype[211]=LJ14, c6A= 4.34922716e-03, c12A= 1.07007298e-05, c6B= 4.34922716e-03, c12B= 1.07007298e-05 39: reppow = 12 39: fudgeQQ = 0.5 39: cmap 39: atomtypes: 39: atomtype[ 0]={atomnumber= 7} 39: atomtype[ 1]={atomnumber= 1} 39: atomtype[ 2]={atomnumber= 6} 39: atomtype[ 3]={atomnumber= 1} 39: atomtype[ 4]={atomnumber= 6} 39: atomtype[ 5]={atomnumber= 8} 39: atomtype[ 6]={atomnumber= 6} 39: atomtype[ 7]={atomnumber= 1} 39: atomtype[ 8]={atomnumber= 6} 39: atomtype[ 9]={atomnumber= 16} 39: moltype (0): 39: name="Protein_chain_B" 39: atoms: 39: atom (156): 39: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 39: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 39: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 39: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 39: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6} 39: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 39: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 39: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 39: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 39: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 39: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 39: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 39: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 39: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 39: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 39: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6} 39: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 39: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 39: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 39: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 39: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 39: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 39: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6} 39: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8} 39: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7} 39: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1} 39: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6} 39: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 39: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6} 39: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 39: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 39: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 39: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 39: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 39: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 39: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 39: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 39: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 39: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6} 39: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8} 39: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7} 39: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1} 39: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6} 39: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 39: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6} 39: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 39: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 39: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 39: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 39: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 39: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 39: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 39: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 39: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 39: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 39: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 39: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 39: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 39: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6} 39: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8} 39: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7} 39: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1} 39: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6} 39: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 39: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 39: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6} 39: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8} 39: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7} 39: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1} 39: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6} 39: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 39: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6} 39: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 39: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 39: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6} 39: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 39: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 39: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6} 39: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 39: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 39: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7} 39: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1} 39: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6} 39: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 39: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 39: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 39: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 39: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 39: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 39: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6} 39: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8} 39: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7} 39: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1} 39: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6} 39: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 39: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6} 39: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 39: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 39: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16} 39: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1} 39: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6} 39: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8} 39: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7} 39: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1} 39: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6} 39: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 39: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6} 39: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 39: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 39: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6} 39: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 39: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 39: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6} 39: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 39: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 39: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6} 39: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8} 39: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7} 39: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1} 39: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6} 39: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6} 39: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6} 39: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 39: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 39: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 39: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6} 39: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8} 39: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7} 39: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1} 39: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6} 39: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 39: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6} 39: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 39: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 39: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 39: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6} 39: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8} 39: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7} 39: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1} 39: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6} 39: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 39: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6} 39: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 39: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 39: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 39: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6} 39: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8} 39: atom (156): 39: atom[0]={name="N"} 39: atom[1]={name="H1"} 39: atom[2]={name="H2"} 39: atom[3]={name="H3"} 39: atom[4]={name="CA"} 39: atom[5]={name="HA"} 39: atom[6]={name="CB"} 39: atom[7]={name="HB1"} 39: atom[8]={name="HB2"} 39: atom[9]={name="CG"} 39: atom[10]={name="HG1"} 39: atom[11]={name="HG2"} 39: atom[12]={name="CD"} 39: atom[13]={name="HD1"} 39: atom[14]={name="HD2"} 39: atom[15]={name="CE"} 39: atom[16]={name="HE1"} 39: atom[17]={name="HE2"} 39: atom[18]={name="NZ"} 39: atom[19]={name="HZ1"} 39: atom[20]={name="HZ2"} 39: atom[21]={name="HZ3"} 39: atom[22]={name="C"} 39: atom[23]={name="O"} 39: atom[24]={name="N"} 39: atom[25]={name="H"} 39: atom[26]={name="CA"} 39: atom[27]={name="HA"} 39: atom[28]={name="CB"} 39: atom[29]={name="HB"} 39: atom[30]={name="CG1"} 39: atom[31]={name="HG11"} 39: atom[32]={name="HG12"} 39: atom[33]={name="HG13"} 39: atom[34]={name="CG2"} 39: atom[35]={name="HG21"} 39: atom[36]={name="HG22"} 39: atom[37]={name="HG23"} 39: atom[38]={name="C"} 39: atom[39]={name="O"} 39: atom[40]={name="N"} 39: atom[41]={name="H"} 39: atom[42]={name="CA"} 39: atom[43]={name="HA"} 39: atom[44]={name="CB"} 39: atom[45]={name="HB1"} 39: atom[46]={name="HB2"} 39: atom[47]={name="CG"} 39: atom[48]={name="CD1"} 39: atom[49]={name="HD1"} 39: atom[50]={name="CD2"} 39: atom[51]={name="HD2"} 39: atom[52]={name="CE1"} 39: atom[53]={name="HE1"} 39: atom[54]={name="CE2"} 39: atom[55]={name="HE2"} 39: atom[56]={name="CZ"} 39: atom[57]={name="HZ"} 39: atom[58]={name="C"} 39: atom[59]={name="O"} 39: atom[60]={name="N"} 39: atom[61]={name="H"} 39: atom[62]={name="CA"} 39: atom[63]={name="HA1"} 39: atom[64]={name="HA2"} 39: atom[65]={name="C"} 39: atom[66]={name="O"} 39: atom[67]={name="N"} 39: atom[68]={name="H"} 39: atom[69]={name="CA"} 39: atom[70]={name="HA"} 39: atom[71]={name="CB"} 39: atom[72]={name="HB1"} 39: atom[73]={name="HB2"} 39: atom[74]={name="CG"} 39: atom[75]={name="HG1"} 39: atom[76]={name="HG2"} 39: atom[77]={name="CD"} 39: atom[78]={name="HD1"} 39: atom[79]={name="HD2"} 39: atom[80]={name="NE"} 39: atom[81]={name="HE"} 39: atom[82]={name="CZ"} 39: atom[83]={name="NH1"} 39: atom[84]={name="HH11"} 39: atom[85]={name="HH12"} 39: atom[86]={name="NH2"} 39: atom[87]={name="HH21"} 39: atom[88]={name="HH22"} 39: atom[89]={name="C"} 39: atom[90]={name="O"} 39: atom[91]={name="N"} 39: atom[92]={name="H"} 39: atom[93]={name="CA"} 39: atom[94]={name="HA"} 39: atom[95]={name="CB"} 39: atom[96]={name="HB1"} 39: atom[97]={name="HB2"} 39: atom[98]={name="SG"} 39: atom[99]={name="HG"} 39: atom[100]={name="C"} 39: atom[101]={name="O"} 39: atom[102]={name="N"} 39: atom[103]={name="H"} 39: atom[104]={name="CA"} 39: atom[105]={name="HA"} 39: atom[106]={name="CB"} 39: atom[107]={name="HB1"} 39: atom[108]={name="HB2"} 39: atom[109]={name="CG"} 39: atom[110]={name="HG1"} 39: atom[111]={name="HG2"} 39: atom[112]={name="CD"} 39: atom[113]={name="OE1"} 39: atom[114]={name="OE2"} 39: atom[115]={name="C"} 39: atom[116]={name="O"} 39: atom[117]={name="N"} 39: atom[118]={name="H"} 39: atom[119]={name="CA"} 39: atom[120]={name="HA"} 39: atom[121]={name="CB"} 39: atom[122]={name="HB1"} 39: atom[123]={name="HB2"} 39: atom[124]={name="CG"} 39: atom[125]={name="HG"} 39: atom[126]={name="CD1"} 39: atom[127]={name="HD11"} 39: atom[128]={name="HD12"} 39: atom[129]={name="HD13"} 39: atom[130]={name="CD2"} 39: atom[131]={name="HD21"} 39: atom[132]={name="HD22"} 39: atom[133]={name="HD23"} 39: atom[134]={name="C"} 39: atom[135]={name="O"} 39: atom[136]={name="N"} 39: atom[137]={name="H"} 39: atom[138]={name="CA"} 39: atom[139]={name="HA"} 39: atom[140]={name="CB"} 39: atom[141]={name="HB1"} 39: atom[142]={name="HB2"} 39: atom[143]={name="HB3"} 39: atom[144]={name="C"} 39: atom[145]={name="O"} 39: atom[146]={name="N"} 39: atom[147]={name="H"} 39: atom[148]={name="CA"} 39: atom[149]={name="HA"} 39: atom[150]={name="CB"} 39: atom[151]={name="HB1"} 39: atom[152]={name="HB2"} 39: atom[153]={name="HB3"} 39: atom[154]={name="C"} 39: atom[155]={name="O"} 39: type (156): 39: type[0]={name="opls_287",nameB="opls_287"} 39: type[1]={name="opls_290",nameB="opls_290"} 39: type[2]={name="opls_290",nameB="opls_290"} 39: type[3]={name="opls_290",nameB="opls_290"} 39: type[4]={name="opls_293B",nameB="opls_293B"} 39: type[5]={name="opls_140",nameB="opls_140"} 39: type[6]={name="opls_136",nameB="opls_136"} 39: type[7]={name="opls_140",nameB="opls_140"} 39: type[8]={name="opls_140",nameB="opls_140"} 39: type[9]={name="opls_136",nameB="opls_136"} 39: type[10]={name="opls_140",nameB="opls_140"} 39: type[11]={name="opls_140",nameB="opls_140"} 39: type[12]={name="opls_136",nameB="opls_136"} 39: type[13]={name="opls_140",nameB="opls_140"} 39: type[14]={name="opls_140",nameB="opls_140"} 39: type[15]={name="opls_292",nameB="opls_292"} 39: type[16]={name="opls_140",nameB="opls_140"} 39: type[17]={name="opls_140",nameB="opls_140"} 39: type[18]={name="opls_287",nameB="opls_287"} 39: type[19]={name="opls_290",nameB="opls_290"} 39: type[20]={name="opls_290",nameB="opls_290"} 39: type[21]={name="opls_290",nameB="opls_290"} 39: type[22]={name="opls_235",nameB="opls_235"} 39: type[23]={name="opls_236",nameB="opls_236"} 39: type[24]={name="opls_238",nameB="opls_238"} 39: type[25]={name="opls_241",nameB="opls_241"} 39: type[26]={name="opls_224B",nameB="opls_224B"} 39: type[27]={name="opls_140",nameB="opls_140"} 39: type[28]={name="opls_137",nameB="opls_137"} 39: type[29]={name="opls_140",nameB="opls_140"} 39: type[30]={name="opls_135",nameB="opls_135"} 39: type[31]={name="opls_140",nameB="opls_140"} 39: type[32]={name="opls_140",nameB="opls_140"} 39: type[33]={name="opls_140",nameB="opls_140"} 39: type[34]={name="opls_135",nameB="opls_135"} 39: type[35]={name="opls_140",nameB="opls_140"} 39: type[36]={name="opls_140",nameB="opls_140"} 39: type[37]={name="opls_140",nameB="opls_140"} 39: type[38]={name="opls_235",nameB="opls_235"} 39: type[39]={name="opls_236",nameB="opls_236"} 39: type[40]={name="opls_238",nameB="opls_238"} 39: type[41]={name="opls_241",nameB="opls_241"} 39: type[42]={name="opls_224B",nameB="opls_224B"} 39: type[43]={name="opls_140",nameB="opls_140"} 39: type[44]={name="opls_149",nameB="opls_149"} 39: type[45]={name="opls_140",nameB="opls_140"} 39: type[46]={name="opls_140",nameB="opls_140"} 39: type[47]={name="opls_145",nameB="opls_145"} 39: type[48]={name="opls_145",nameB="opls_145"} 39: type[49]={name="opls_146",nameB="opls_146"} 39: type[50]={name="opls_145",nameB="opls_145"} 39: type[51]={name="opls_146",nameB="opls_146"} 39: type[52]={name="opls_145",nameB="opls_145"} 39: type[53]={name="opls_146",nameB="opls_146"} 39: type[54]={name="opls_145",nameB="opls_145"} 39: type[55]={name="opls_146",nameB="opls_146"} 39: type[56]={name="opls_145",nameB="opls_145"} 39: type[57]={name="opls_146",nameB="opls_146"} 39: type[58]={name="opls_235",nameB="opls_235"} 39: type[59]={name="opls_236",nameB="opls_236"} 39: type[60]={name="opls_238",nameB="opls_238"} 39: type[61]={name="opls_241",nameB="opls_241"} 39: type[62]={name="opls_223B",nameB="opls_223B"} 39: type[63]={name="opls_140",nameB="opls_140"} 39: type[64]={name="opls_140",nameB="opls_140"} 39: type[65]={name="opls_235",nameB="opls_235"} 39: type[66]={name="opls_236",nameB="opls_236"} 39: type[67]={name="opls_238",nameB="opls_238"} 39: type[68]={name="opls_241",nameB="opls_241"} 39: type[69]={name="opls_224B",nameB="opls_224B"} 39: type[70]={name="opls_140",nameB="opls_140"} 39: type[71]={name="opls_136",nameB="opls_136"} 39: type[72]={name="opls_140",nameB="opls_140"} 39: type[73]={name="opls_140",nameB="opls_140"} 39: type[74]={name="opls_308",nameB="opls_308"} 39: type[75]={name="opls_140",nameB="opls_140"} 39: type[76]={name="opls_140",nameB="opls_140"} 39: type[77]={name="opls_307",nameB="opls_307"} 39: type[78]={name="opls_140",nameB="opls_140"} 39: type[79]={name="opls_140",nameB="opls_140"} 39: type[80]={name="opls_303",nameB="opls_303"} 39: type[81]={name="opls_304",nameB="opls_304"} 39: type[82]={name="opls_302",nameB="opls_302"} 39: type[83]={name="opls_300",nameB="opls_300"} 39: type[84]={name="opls_301",nameB="opls_301"} 39: type[85]={name="opls_301",nameB="opls_301"} 39: type[86]={name="opls_300",nameB="opls_300"} 39: type[87]={name="opls_301",nameB="opls_301"} 39: type[88]={name="opls_301",nameB="opls_301"} 39: type[89]={name="opls_235",nameB="opls_235"} 39: type[90]={name="opls_236",nameB="opls_236"} 39: type[91]={name="opls_238",nameB="opls_238"} 39: type[92]={name="opls_241",nameB="opls_241"} 39: type[93]={name="opls_224B",nameB="opls_224B"} 39: type[94]={name="opls_140",nameB="opls_140"} 39: type[95]={name="opls_206",nameB="opls_206"} 39: type[96]={name="opls_140",nameB="opls_140"} 39: type[97]={name="opls_140",nameB="opls_140"} 39: type[98]={name="opls_200",nameB="opls_200"} 39: type[99]={name="opls_204",nameB="opls_204"} 39: type[100]={name="opls_235",nameB="opls_235"} 39: type[101]={name="opls_236",nameB="opls_236"} 39: type[102]={name="opls_238",nameB="opls_238"} 39: type[103]={name="opls_241",nameB="opls_241"} 39: type[104]={name="opls_224B",nameB="opls_224B"} 39: type[105]={name="opls_140",nameB="opls_140"} 39: type[106]={name="opls_136",nameB="opls_136"} 39: type[107]={name="opls_140",nameB="opls_140"} 39: type[108]={name="opls_140",nameB="opls_140"} 39: type[109]={name="opls_274",nameB="opls_274"} 39: type[110]={name="opls_140",nameB="opls_140"} 39: type[111]={name="opls_140",nameB="opls_140"} 39: type[112]={name="opls_271",nameB="opls_271"} 39: type[113]={name="opls_272",nameB="opls_272"} 39: type[114]={name="opls_272",nameB="opls_272"} 39: type[115]={name="opls_235",nameB="opls_235"} 39: type[116]={name="opls_236",nameB="opls_236"} 39: type[117]={name="opls_238",nameB="opls_238"} 39: type[118]={name="opls_241",nameB="opls_241"} 39: type[119]={name="opls_224B",nameB="opls_224B"} 39: type[120]={name="opls_140",nameB="opls_140"} 39: type[121]={name="opls_136",nameB="opls_136"} 39: type[122]={name="opls_140",nameB="opls_140"} 39: type[123]={name="opls_140",nameB="opls_140"} 39: type[124]={name="opls_137",nameB="opls_137"} 39: type[125]={name="opls_140",nameB="opls_140"} 39: type[126]={name="opls_135",nameB="opls_135"} 39: type[127]={name="opls_140",nameB="opls_140"} 39: type[128]={name="opls_140",nameB="opls_140"} 39: type[129]={name="opls_140",nameB="opls_140"} 39: type[130]={name="opls_135",nameB="opls_135"} 39: type[131]={name="opls_140",nameB="opls_140"} 39: type[132]={name="opls_140",nameB="opls_140"} 39: type[133]={name="opls_140",nameB="opls_140"} 39: type[134]={name="opls_235",nameB="opls_235"} 39: type[135]={name="opls_236",nameB="opls_236"} 39: type[136]={name="opls_238",nameB="opls_238"} 39: type[137]={name="opls_241",nameB="opls_241"} 39: type[138]={name="opls_224B",nameB="opls_224B"} 39: type[139]={name="opls_140",nameB="opls_140"} 39: type[140]={name="opls_135",nameB="opls_135"} 39: type[141]={name="opls_140",nameB="opls_140"} 39: type[142]={name="opls_140",nameB="opls_140"} 39: type[143]={name="opls_140",nameB="opls_140"} 39: type[144]={name="opls_235",nameB="opls_235"} 39: type[145]={name="opls_236",nameB="opls_236"} 39: type[146]={name="opls_238",nameB="opls_238"} 39: type[147]={name="opls_241",nameB="opls_241"} 39: type[148]={name="opls_224B",nameB="opls_224B"} 39: type[149]={name="opls_140",nameB="opls_140"} 39: type[150]={name="opls_135",nameB="opls_135"} 39: type[151]={name="opls_140",nameB="opls_140"} 39: type[152]={name="opls_140",nameB="opls_140"} 39: type[153]={name="opls_140",nameB="opls_140"} 39: type[154]={name="opls_235",nameB="opls_235"} 39: type[155]={name="opls_236",nameB="opls_236"} 39: residue (10): 39: residue[0]={name="LYS", nr=1, ic=' '} 39: residue[1]={name="VAL", nr=2, ic=' '} 39: residue[2]={name="PHE", nr=3, ic=' '} 39: residue[3]={name="GLY", nr=4, ic=' '} 39: residue[4]={name="ARG", nr=5, ic=' '} 39: residue[5]={name="CYS", nr=6, ic=' '} 39: residue[6]={name="GLU", nr=7, ic=' '} 39: residue[7]={name="LEU", nr=8, ic=' '} 39: residue[8]={name="ALA", nr=9, ic=' '} 39: residue[9]={name="ALA", nr=10, ic=' '} 39: excls: 39: nr=156 39: nra=1828 39: excls[0][0..12]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 39: excls[1][13..20]={0, 1, 2, 3, 4, 5, 6, 22} 39: excls[2][21..28]={0, 1, 2, 3, 4, 5, 6, 22} 39: excls[3][29..36]={0, 1, 2, 3, 4, 5, 6, 22} 39: excls[4][37..54]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 39: 23, 24, 25, 26} 39: excls[5][55..67]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 39: excls[6][68..86]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 39: 14, 15, 22, 23, 24} 39: excls[7][87..97]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 39: excls[8][98..108]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 39: excls[9][109..125]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 39: 16, 17, 18, 22} 39: excls[10][126..136]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 39: excls[11][137..147]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 39: excls[12][148..164]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 39: 17, 18, 19, 20, 21} 39: excls[13][165..175]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 39: excls[14][176..186]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 39: excls[15][187..200]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 39: 19, 20, 21} 39: excls[16][201..211]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 39: excls[17][212..222]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 39: excls[18][223..233]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 39: excls[19][234..241]={12, 15, 16, 17, 18, 19, 20, 21} 39: excls[20][242..249]={12, 15, 16, 17, 18, 19, 20, 21} 39: excls[21][250..257]={12, 15, 16, 17, 18, 19, 20, 21} 39: excls[22][258..275]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 39: 25, 26, 27, 28, 38} 39: excls[23][276..284]={0, 4, 5, 6, 22, 23, 24, 25, 26} 39: excls[24][285..301]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 39: 30, 34, 38, 39, 40} 39: excls[25][302..310]={4, 22, 23, 24, 25, 26, 27, 28, 38} 39: excls[26][311..332]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42} 39: excls[27][333..344]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 39: 40} 39: excls[28][345..362]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39: 34, 35, 36, 37, 38, 39, 40} 39: excls[29][363..376]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39: 36, 37, 38} 39: excls[30][377..390]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39: 36, 37, 38} 39: excls[31][391..398]={26, 28, 29, 30, 31, 32, 33, 34} 39: excls[32][399..406]={26, 28, 29, 30, 31, 32, 33, 34} 39: excls[33][407..414]={26, 28, 29, 30, 31, 32, 33, 34} 39: excls[34][415..428]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39: 36, 37, 38} 39: excls[35][429..436]={26, 28, 29, 30, 34, 35, 36, 37} 39: excls[36][437..444]={26, 28, 29, 30, 34, 35, 36, 37} 39: excls[37][445..452]={26, 28, 29, 30, 34, 35, 36, 37} 39: excls[38][453..469]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 39: 40, 41, 42, 43, 44, 58} 39: excls[39][470..478]={24, 26, 27, 28, 38, 39, 40, 41, 42} 39: excls[40][479..495]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 39: 45, 46, 47, 58, 59, 60} 39: excls[41][496..504]={26, 38, 39, 40, 41, 42, 43, 44, 58} 39: excls[42][505..522]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 39: 48, 50, 58, 59, 60, 61, 62} 39: excls[43][523..534]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 39: 60} 39: excls[44][535..552]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 39: 50, 51, 52, 54, 58, 59, 60} 39: excls[45][553..562]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 39: excls[46][563..572]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 39: excls[47][573..589]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 39: 52, 53, 54, 55, 56, 58} 39: excls[48][590..603]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 39: 54, 56, 57} 39: excls[49][604..611]={44, 47, 48, 49, 50, 52, 53, 56} 39: excls[50][612..625]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 39: 55, 56, 57} 39: excls[51][626..633]={44, 47, 48, 50, 51, 54, 55, 56} 39: excls[52][634..644]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57} 39: excls[53][645..652]={47, 48, 49, 52, 53, 54, 56, 57} 39: excls[54][653..663]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57} 39: excls[55][664..671]={47, 50, 51, 52, 54, 55, 56, 57} 39: excls[56][672..682]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57} 39: excls[57][683..690]={48, 50, 52, 53, 54, 55, 56, 57} 39: excls[58][691..707]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 39: 60, 61, 62, 63, 64, 65} 39: excls[59][708..716]={40, 42, 43, 44, 58, 59, 60, 61, 62} 39: excls[60][717..730]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64, 39: 65, 66, 67} 39: excls[61][731..739]={42, 58, 59, 60, 61, 62, 63, 64, 65} 39: excls[62][740..752]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 39: 68, 69} 39: excls[63][753..761]={58, 60, 61, 62, 63, 64, 65, 66, 67} 39: excls[64][762..770]={58, 60, 61, 62, 63, 64, 65, 66, 67} 39: excls[65][771..784]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 39: 70, 71, 89} 39: excls[66][785..793]={60, 62, 63, 64, 65, 66, 67, 68, 69} 39: excls[67][794..810]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 39: 72, 73, 74, 89, 90, 91} 39: excls[68][811..819]={62, 65, 66, 67, 68, 69, 70, 71, 89} 39: excls[69][820..838]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 39: 75, 76, 77, 89, 90, 91, 92, 93} 39: excls[70][839..850]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 39: 91} 39: excls[71][851..868]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 39: 77, 78, 79, 80, 89, 90, 91} 39: excls[72][869..879]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 39: excls[73][880..890]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 39: excls[74][891..906]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 39: 79, 80, 81, 82, 89} 39: excls[75][907..917]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 39: excls[76][918..928]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 39: excls[77][929..943]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 39: 81, 82, 83, 86} 39: excls[78][944..953]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 39: excls[79][954..963]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 39: excls[80][964..979]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 39: 84, 85, 86, 87, 88} 39: excls[81][980..988]={74, 77, 78, 79, 80, 81, 82, 83, 86} 39: excls[82][989..1001]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 39: 86, 87, 88} 39: excls[83][1002..1011]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 39: excls[84][1012..1017]={80, 82, 83, 84, 85, 86} 39: excls[85][1018..1023]={80, 82, 83, 84, 85, 86} 39: excls[86][1024..1033]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 39: excls[87][1034..1039]={80, 82, 83, 86, 87, 88} 39: excls[88][1040..1045]={80, 82, 83, 86, 87, 88} 39: excls[89][1046..1062]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 39: 90, 91, 92, 93, 94, 95, 100} 39: excls[90][1063..1071]={67, 69, 70, 71, 89, 90, 91, 92, 93} 39: excls[91][1072..1088]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 39: 95, 96, 97, 98, 100, 101, 102} 39: excls[92][1089..1097]={69, 89, 90, 91, 92, 93, 94, 95, 100} 39: excls[93][1098..1114]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 39: 98, 99, 100, 101, 102, 103, 104} 39: excls[94][1115..1126]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 39: 101, 102} 39: excls[95][1127..1139]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 39: 100, 101, 102} 39: excls[96][1140..1148]={91, 93, 94, 95, 96, 97, 98, 99, 100} 39: excls[97][1149..1157]={91, 93, 94, 95, 96, 97, 98, 99, 100} 39: excls[98][1158..1166]={91, 93, 94, 95, 96, 97, 98, 99, 100} 39: excls[99][1167..1172]={93, 95, 96, 97, 98, 99} 39: excls[100][1173..1189]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 39: 101, 102, 103, 104, 105, 106, 115} 39: excls[101][1190..1198]={91, 93, 94, 95, 100, 101, 102, 103, 104} 39: excls[102][1199..1215]={91, 93, 94, 95, 100, 101, 102, 103, 104, 39: 105, 106, 107, 108, 109, 115, 116, 117} 39: excls[103][1216..1224]={93, 100, 101, 102, 103, 104, 105, 106, 39: 115} 39: excls[104][1225..1243]={93, 100, 101, 102, 103, 104, 105, 106, 39: 107, 108, 109, 110, 111, 112, 115, 116, 117, 118, 119} 39: excls[105][1244..1255]={100, 102, 103, 104, 105, 106, 107, 108, 39: 109, 115, 116, 117} 39: excls[106][1256..1272]={100, 102, 103, 104, 105, 106, 107, 108, 39: 109, 110, 111, 112, 113, 114, 115, 116, 117} 39: excls[107][1273..1283]={102, 104, 105, 106, 107, 108, 109, 110, 39: 111, 112, 115} 39: excls[108][1284..1294]={102, 104, 105, 106, 107, 108, 109, 110, 39: 111, 112, 115} 39: excls[109][1295..1307]={102, 104, 105, 106, 107, 108, 109, 110, 39: 111, 112, 113, 114, 115} 39: excls[110][1308..1317]={104, 106, 107, 108, 109, 110, 111, 112, 39: 113, 114} 39: excls[111][1318..1327]={104, 106, 107, 108, 109, 110, 111, 112, 39: 113, 114} 39: excls[112][1328..1337]={104, 106, 107, 108, 109, 110, 111, 112, 39: 113, 114} 39: excls[113][1338..1344]={106, 109, 110, 111, 112, 113, 114} 39: excls[114][1345..1351]={106, 109, 110, 111, 112, 113, 114} 39: excls[115][1352..1368]={100, 102, 103, 104, 105, 106, 107, 108, 39: 109, 115, 116, 117, 118, 119, 120, 121, 134} 39: excls[116][1369..1377]={102, 104, 105, 106, 115, 116, 117, 118, 39: 119} 39: excls[117][1378..1394]={102, 104, 105, 106, 115, 116, 117, 118, 39: 119, 120, 121, 122, 123, 124, 134, 135, 136} 39: excls[118][1395..1403]={104, 115, 116, 117, 118, 119, 120, 121, 39: 134} 39: excls[119][1404..1422]={104, 115, 116, 117, 118, 119, 120, 121, 39: 122, 123, 124, 125, 126, 130, 134, 135, 136, 137, 138} 39: excls[120][1423..1434]={115, 117, 118, 119, 120, 121, 122, 123, 39: 124, 134, 135, 136} 39: excls[121][1435..1455]={115, 117, 118, 119, 120, 121, 122, 123, 39: 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 39: 136} 39: excls[122][1456..1466]={117, 119, 120, 121, 122, 123, 124, 125, 39: 126, 130, 134} 39: excls[123][1467..1477]={117, 119, 120, 121, 122, 123, 124, 125, 39: 126, 130, 134} 39: excls[124][1478..1494]={117, 119, 120, 121, 122, 123, 124, 125, 39: 126, 127, 128, 129, 130, 131, 132, 133, 134} 39: excls[125][1495..1508]={119, 121, 122, 123, 124, 125, 126, 127, 39: 128, 129, 130, 131, 132, 133} 39: excls[126][1509..1522]={119, 121, 122, 123, 124, 125, 126, 127, 39: 128, 129, 130, 131, 132, 133} 39: excls[127][1523..1530]={121, 124, 125, 126, 127, 128, 129, 130} 39: excls[128][1531..1538]={121, 124, 125, 126, 127, 128, 129, 130} 39: excls[129][1539..1546]={121, 124, 125, 126, 127, 128, 129, 130} 39: excls[130][1547..1560]={119, 121, 122, 123, 124, 125, 126, 127, 39: 128, 129, 130, 131, 132, 133} 39: excls[131][1561..1568]={121, 124, 125, 126, 130, 131, 132, 133} 39: excls[132][1569..1576]={121, 124, 125, 126, 130, 131, 132, 133} 39: excls[133][1577..1584]={121, 124, 125, 126, 130, 131, 132, 133} 39: excls[134][1585..1601]={115, 117, 118, 119, 120, 121, 122, 123, 39: 124, 134, 135, 136, 137, 138, 139, 140, 144} 39: excls[135][1602..1610]={117, 119, 120, 121, 134, 135, 136, 137, 39: 138} 39: excls[136][1611..1627]={117, 119, 120, 121, 134, 135, 136, 137, 39: 138, 139, 140, 141, 142, 143, 144, 145, 146} 39: excls[137][1628..1636]={119, 134, 135, 136, 137, 138, 139, 140, 39: 144} 39: excls[138][1637..1652]={119, 134, 135, 136, 137, 138, 139, 140, 39: 141, 142, 143, 144, 145, 146, 147, 148} 39: excls[139][1653..1664]={134, 136, 137, 138, 139, 140, 141, 142, 39: 143, 144, 145, 146} 39: excls[140][1665..1676]={134, 136, 137, 138, 139, 140, 141, 142, 39: 143, 144, 145, 146} 39: excls[141][1677..1684]={136, 138, 139, 140, 141, 142, 143, 144} 39: excls[142][1685..1692]={136, 138, 139, 140, 141, 142, 143, 144} 39: excls[143][1693..1700]={136, 138, 139, 140, 141, 142, 143, 144} 39: excls[144][1701..1717]={134, 136, 137, 138, 139, 140, 141, 142, 39: 143, 144, 145, 146, 147, 148, 149, 150, 154} 39: excls[145][1718..1726]={136, 138, 139, 140, 144, 145, 146, 147, 39: 148} 39: excls[146][1727..1742]={136, 138, 139, 140, 144, 145, 146, 147, 39: 148, 149, 150, 151, 152, 153, 154, 155} 39: excls[147][1743..1751]={138, 144, 145, 146, 147, 148, 149, 150, 39: 154} 39: excls[148][1752..1764]={138, 144, 145, 146, 147, 148, 149, 150, 39: 151, 152, 153, 154, 155} 39: excls[149][1765..1775]={144, 146, 147, 148, 149, 150, 151, 152, 39: 153, 154, 155} 39: excls[150][1776..1786]={144, 146, 147, 148, 149, 150, 151, 152, 39: 153, 154, 155} 39: excls[151][1787..1794]={146, 148, 149, 150, 151, 152, 153, 154} 39: excls[152][1795..1802]={146, 148, 149, 150, 151, 152, 153, 154} 39: excls[153][1803..1810]={146, 148, 149, 150, 151, 152, 153, 154} 39: excls[154][1811..1821]={144, 146, 147, 148, 149, 150, 151, 152, 39: 153, 154, 155} 39: excls[155][1822..1827]={146, 148, 149, 150, 154, 155} 39: Bond: 39: nr: 468 39: iatoms: 39: 0 type=100 (BONDS) 0 1 39: 1 type=100 (BONDS) 0 2 39: 2 type=100 (BONDS) 0 3 39: 3 type=101 (BONDS) 0 4 39: 4 type=102 (BONDS) 4 5 39: 5 type=103 (BONDS) 4 6 39: 6 type=104 (BONDS) 4 22 39: 7 type=102 (BONDS) 6 7 39: 8 type=102 (BONDS) 6 8 39: 9 type=103 (BONDS) 6 9 39: 10 type=102 (BONDS) 9 10 39: 11 type=102 (BONDS) 9 11 39: 12 type=103 (BONDS) 9 12 39: 13 type=102 (BONDS) 12 13 39: 14 type=102 (BONDS) 12 14 39: 15 type=103 (BONDS) 12 15 39: 16 type=102 (BONDS) 15 16 39: 17 type=102 (BONDS) 15 17 39: 18 type=101 (BONDS) 15 18 39: 19 type=100 (BONDS) 18 19 39: 20 type=100 (BONDS) 18 20 39: 21 type=100 (BONDS) 18 21 39: 22 type=105 (BONDS) 22 23 39: 23 type=106 (BONDS) 22 24 39: 24 type=100 (BONDS) 24 25 39: 25 type=107 (BONDS) 24 26 39: 26 type=102 (BONDS) 26 27 39: 27 type=103 (BONDS) 26 28 39: 28 type=104 (BONDS) 26 38 39: 29 type=102 (BONDS) 28 29 39: 30 type=103 (BONDS) 28 30 39: 31 type=103 (BONDS) 28 34 39: 32 type=102 (BONDS) 30 31 39: 33 type=102 (BONDS) 30 32 39: 34 type=102 (BONDS) 30 33 39: 35 type=102 (BONDS) 34 35 39: 36 type=102 (BONDS) 34 36 39: 37 type=102 (BONDS) 34 37 39: 38 type=105 (BONDS) 38 39 39: 39 type=106 (BONDS) 38 40 39: 40 type=100 (BONDS) 40 41 39: 41 type=107 (BONDS) 40 42 39: 42 type=102 (BONDS) 42 43 39: 43 type=103 (BONDS) 42 44 39: 44 type=104 (BONDS) 42 58 39: 45 type=102 (BONDS) 44 45 39: 46 type=102 (BONDS) 44 46 39: 47 type=108 (BONDS) 44 47 39: 48 type=109 (BONDS) 47 48 39: 49 type=109 (BONDS) 47 50 39: 50 type=110 (BONDS) 48 49 39: 51 type=109 (BONDS) 48 52 39: 52 type=110 (BONDS) 50 51 39: 53 type=109 (BONDS) 50 54 39: 54 type=110 (BONDS) 52 53 39: 55 type=109 (BONDS) 52 56 39: 56 type=110 (BONDS) 54 55 39: 57 type=109 (BONDS) 54 56 39: 58 type=110 (BONDS) 56 57 39: 59 type=105 (BONDS) 58 59 39: 60 type=106 (BONDS) 58 60 39: 61 type=100 (BONDS) 60 61 39: 62 type=107 (BONDS) 60 62 39: 63 type=102 (BONDS) 62 63 39: 64 type=102 (BONDS) 62 64 39: 65 type=104 (BONDS) 62 65 39: 66 type=105 (BONDS) 65 66 39: 67 type=106 (BONDS) 65 67 39: 68 type=100 (BONDS) 67 68 39: 69 type=107 (BONDS) 67 69 39: 70 type=102 (BONDS) 69 70 39: 71 type=103 (BONDS) 69 71 39: 72 type=104 (BONDS) 69 89 39: 73 type=102 (BONDS) 71 72 39: 74 type=102 (BONDS) 71 73 39: 75 type=103 (BONDS) 71 74 39: 76 type=102 (BONDS) 74 75 39: 77 type=102 (BONDS) 74 76 39: 78 type=103 (BONDS) 74 77 39: 79 type=102 (BONDS) 77 78 39: 80 type=102 (BONDS) 77 79 39: 81 type=111 (BONDS) 77 80 39: 82 type=100 (BONDS) 80 81 39: 83 type=112 (BONDS) 80 82 39: 84 type=112 (BONDS) 82 83 39: 85 type=112 (BONDS) 82 86 39: 86 type=100 (BONDS) 83 84 39: 87 type=100 (BONDS) 83 85 39: 88 type=100 (BONDS) 86 87 39: 89 type=100 (BONDS) 86 88 39: 90 type=105 (BONDS) 89 90 39: 91 type=106 (BONDS) 89 91 39: 92 type=100 (BONDS) 91 92 39: 93 type=107 (BONDS) 91 93 39: 94 type=102 (BONDS) 93 94 39: 95 type=103 (BONDS) 93 95 39: 96 type=104 (BONDS) 93 100 39: 97 type=102 (BONDS) 95 96 39: 98 type=102 (BONDS) 95 97 39: 99 type=113 (BONDS) 95 98 39: 100 type=114 (BONDS) 98 99 39: 101 type=105 (BONDS) 100 101 39: 102 type=106 (BONDS) 100 102 39: 103 type=100 (BONDS) 102 103 39: 104 type=107 (BONDS) 102 104 39: 105 type=102 (BONDS) 104 105 39: 106 type=103 (BONDS) 104 106 39: 107 type=104 (BONDS) 104 115 39: 108 type=102 (BONDS) 106 107 39: 109 type=102 (BONDS) 106 108 39: 110 type=103 (BONDS) 106 109 39: 111 type=102 (BONDS) 109 110 39: 112 type=102 (BONDS) 109 111 39: 113 type=104 (BONDS) 109 112 39: 114 type=115 (BONDS) 112 113 39: 115 type=115 (BONDS) 112 114 39: 116 type=105 (BONDS) 115 116 39: 117 type=106 (BONDS) 115 117 39: 118 type=100 (BONDS) 117 118 39: 119 type=107 (BONDS) 117 119 39: 120 type=102 (BONDS) 119 120 39: 121 type=103 (BONDS) 119 121 39: 122 type=104 (BONDS) 119 134 39: 123 type=102 (BONDS) 121 122 39: 124 type=102 (BONDS) 121 123 39: 125 type=103 (BONDS) 121 124 39: 126 type=102 (BONDS) 124 125 39: 127 type=103 (BONDS) 124 126 39: 128 type=103 (BONDS) 124 130 39: 129 type=102 (BONDS) 126 127 39: 130 type=102 (BONDS) 126 128 39: 131 type=102 (BONDS) 126 129 39: 132 type=102 (BONDS) 130 131 39: 133 type=102 (BONDS) 130 132 39: 134 type=102 (BONDS) 130 133 39: 135 type=105 (BONDS) 134 135 39: 136 type=106 (BONDS) 134 136 39: 137 type=100 (BONDS) 136 137 39: 138 type=107 (BONDS) 136 138 39: 139 type=102 (BONDS) 138 139 39: 140 type=103 (BONDS) 138 140 39: 141 type=104 (BONDS) 138 144 39: 142 type=102 (BONDS) 140 141 39: 143 type=102 (BONDS) 140 142 39: 144 type=102 (BONDS) 140 143 39: 145 type=105 (BONDS) 144 145 39: 146 type=106 (BONDS) 144 146 39: 147 type=100 (BONDS) 146 147 39: 148 type=107 (BONDS) 146 148 39: 149 type=102 (BONDS) 148 149 39: 150 type=103 (BONDS) 148 150 39: 151 type=104 (BONDS) 148 154 39: 152 type=102 (BONDS) 150 151 39: 153 type=102 (BONDS) 150 152 39: 154 type=102 (BONDS) 150 153 39: 155 type=105 (BONDS) 154 155 39: G96Bond: 39: nr: 0 39: Morse: 39: nr: 0 39: Cubic Bonds: 39: nr: 0 39: Connect Bonds: 39: nr: 0 39: Harmonic Pot.: 39: nr: 0 39: FENE Bonds: 39: nr: 0 39: Tab. Bonds: 39: nr: 0 39: Tab. Bonds NC: 39: nr: 0 39: Restraint Pot.: 39: nr: 0 39: Angle: 39: nr: 1124 39: iatoms: 39: 0 type=116 (ANGLES) 1 0 2 39: 1 type=116 (ANGLES) 1 0 3 39: 2 type=116 (ANGLES) 1 0 4 39: 3 type=116 (ANGLES) 2 0 3 39: 4 type=116 (ANGLES) 2 0 4 39: 5 type=116 (ANGLES) 3 0 4 39: 6 type=116 (ANGLES) 0 4 5 39: 7 type=117 (ANGLES) 0 4 6 39: 8 type=117 (ANGLES) 0 4 22 39: 9 type=118 (ANGLES) 5 4 6 39: 10 type=116 (ANGLES) 5 4 22 39: 11 type=119 (ANGLES) 6 4 22 39: 12 type=118 (ANGLES) 4 6 7 39: 13 type=118 (ANGLES) 4 6 8 39: 14 type=120 (ANGLES) 4 6 9 39: 15 type=121 (ANGLES) 7 6 8 39: 16 type=118 (ANGLES) 7 6 9 39: 17 type=118 (ANGLES) 8 6 9 39: 18 type=118 (ANGLES) 6 9 10 39: 19 type=118 (ANGLES) 6 9 11 39: 20 type=120 (ANGLES) 6 9 12 39: 21 type=121 (ANGLES) 10 9 11 39: 22 type=118 (ANGLES) 10 9 12 39: 23 type=118 (ANGLES) 11 9 12 39: 24 type=118 (ANGLES) 9 12 13 39: 25 type=118 (ANGLES) 9 12 14 39: 26 type=120 (ANGLES) 9 12 15 39: 27 type=121 (ANGLES) 13 12 14 39: 28 type=118 (ANGLES) 13 12 15 39: 29 type=118 (ANGLES) 14 12 15 39: 30 type=118 (ANGLES) 12 15 16 39: 31 type=118 (ANGLES) 12 15 17 39: 32 type=117 (ANGLES) 12 15 18 39: 33 type=121 (ANGLES) 16 15 17 39: 34 type=116 (ANGLES) 16 15 18 39: 35 type=116 (ANGLES) 17 15 18 39: 36 type=116 (ANGLES) 15 18 19 39: 37 type=116 (ANGLES) 15 18 20 39: 38 type=116 (ANGLES) 15 18 21 39: 39 type=116 (ANGLES) 19 18 20 39: 40 type=116 (ANGLES) 19 18 21 39: 41 type=116 (ANGLES) 20 18 21 39: 42 type=122 (ANGLES) 4 22 23 39: 43 type=123 (ANGLES) 4 22 24 39: 44 type=124 (ANGLES) 23 22 24 39: 45 type=125 (ANGLES) 22 24 25 39: 46 type=126 (ANGLES) 22 24 26 39: 47 type=127 (ANGLES) 25 24 26 39: 48 type=116 (ANGLES) 24 26 27 39: 49 type=128 (ANGLES) 24 26 28 39: 50 type=129 (ANGLES) 24 26 38 39: 51 type=118 (ANGLES) 27 26 28 39: 52 type=116 (ANGLES) 27 26 38 39: 53 type=119 (ANGLES) 28 26 38 39: 54 type=118 (ANGLES) 26 28 29 39: 55 type=120 (ANGLES) 26 28 30 39: 56 type=120 (ANGLES) 26 28 34 39: 57 type=118 (ANGLES) 29 28 30 39: 58 type=118 (ANGLES) 29 28 34 39: 59 type=120 (ANGLES) 30 28 34 39: 60 type=118 (ANGLES) 28 30 31 39: 61 type=118 (ANGLES) 28 30 32 39: 62 type=118 (ANGLES) 28 30 33 39: 63 type=121 (ANGLES) 31 30 32 39: 64 type=121 (ANGLES) 31 30 33 39: 65 type=121 (ANGLES) 32 30 33 39: 66 type=118 (ANGLES) 28 34 35 39: 67 type=118 (ANGLES) 28 34 36 39: 68 type=118 (ANGLES) 28 34 37 39: 69 type=121 (ANGLES) 35 34 36 39: 70 type=121 (ANGLES) 35 34 37 39: 71 type=121 (ANGLES) 36 34 37 39: 72 type=122 (ANGLES) 26 38 39 39: 73 type=123 (ANGLES) 26 38 40 39: 74 type=124 (ANGLES) 39 38 40 39: 75 type=125 (ANGLES) 38 40 41 39: 76 type=126 (ANGLES) 38 40 42 39: 77 type=127 (ANGLES) 41 40 42 39: 78 type=116 (ANGLES) 40 42 43 39: 79 type=128 (ANGLES) 40 42 44 39: 80 type=129 (ANGLES) 40 42 58 39: 81 type=118 (ANGLES) 43 42 44 39: 82 type=116 (ANGLES) 43 42 58 39: 83 type=119 (ANGLES) 44 42 58 39: 84 type=118 (ANGLES) 42 44 45 39: 85 type=118 (ANGLES) 42 44 46 39: 86 type=130 (ANGLES) 42 44 47 39: 87 type=121 (ANGLES) 45 44 46 39: 88 type=116 (ANGLES) 45 44 47 39: 89 type=116 (ANGLES) 46 44 47 39: 90 type=131 (ANGLES) 44 47 48 39: 91 type=131 (ANGLES) 44 47 50 39: 92 type=132 (ANGLES) 48 47 50 39: 93 type=133 (ANGLES) 47 48 49 39: 94 type=132 (ANGLES) 47 48 52 39: 95 type=133 (ANGLES) 49 48 52 39: 96 type=133 (ANGLES) 47 50 51 39: 97 type=132 (ANGLES) 47 50 54 39: 98 type=133 (ANGLES) 51 50 54 39: 99 type=133 (ANGLES) 48 52 53 39: 100 type=132 (ANGLES) 48 52 56 39: 101 type=133 (ANGLES) 53 52 56 39: 102 type=133 (ANGLES) 50 54 55 39: 103 type=132 (ANGLES) 50 54 56 39: 104 type=133 (ANGLES) 55 54 56 39: 105 type=132 (ANGLES) 52 56 54 39: 106 type=133 (ANGLES) 52 56 57 39: 107 type=133 (ANGLES) 54 56 57 39: 108 type=122 (ANGLES) 42 58 59 39: 109 type=123 (ANGLES) 42 58 60 39: 110 type=124 (ANGLES) 59 58 60 39: 111 type=125 (ANGLES) 58 60 61 39: 112 type=126 (ANGLES) 58 60 62 39: 113 type=127 (ANGLES) 61 60 62 39: 114 type=116 (ANGLES) 60 62 63 39: 115 type=116 (ANGLES) 60 62 64 39: 116 type=129 (ANGLES) 60 62 65 39: 117 type=121 (ANGLES) 63 62 64 39: 118 type=116 (ANGLES) 63 62 65 39: 119 type=116 (ANGLES) 64 62 65 39: 120 type=122 (ANGLES) 62 65 66 39: 121 type=123 (ANGLES) 62 65 67 39: 122 type=124 (ANGLES) 66 65 67 39: 123 type=125 (ANGLES) 65 67 68 39: 124 type=126 (ANGLES) 65 67 69 39: 125 type=127 (ANGLES) 68 67 69 39: 126 type=116 (ANGLES) 67 69 70 39: 127 type=128 (ANGLES) 67 69 71 39: 128 type=129 (ANGLES) 67 69 89 39: 129 type=118 (ANGLES) 70 69 71 39: 130 type=116 (ANGLES) 70 69 89 39: 131 type=119 (ANGLES) 71 69 89 39: 132 type=118 (ANGLES) 69 71 72 39: 133 type=118 (ANGLES) 69 71 73 39: 134 type=120 (ANGLES) 69 71 74 39: 135 type=121 (ANGLES) 72 71 73 39: 136 type=118 (ANGLES) 72 71 74 39: 137 type=118 (ANGLES) 73 71 74 39: 138 type=118 (ANGLES) 71 74 75 39: 139 type=118 (ANGLES) 71 74 76 39: 140 type=120 (ANGLES) 71 74 77 39: 141 type=121 (ANGLES) 75 74 76 39: 142 type=118 (ANGLES) 75 74 77 39: 143 type=118 (ANGLES) 76 74 77 39: 144 type=118 (ANGLES) 74 77 78 39: 145 type=118 (ANGLES) 74 77 79 39: 146 type=117 (ANGLES) 74 77 80 39: 147 type=121 (ANGLES) 78 77 79 39: 148 type=116 (ANGLES) 78 77 80 39: 149 type=116 (ANGLES) 79 77 80 39: 150 type=134 (ANGLES) 77 80 81 39: 151 type=135 (ANGLES) 77 80 82 39: 152 type=133 (ANGLES) 81 80 82 39: 153 type=131 (ANGLES) 80 82 83 39: 154 type=131 (ANGLES) 80 82 86 39: 155 type=131 (ANGLES) 83 82 86 39: 156 type=133 (ANGLES) 82 83 84 39: 157 type=133 (ANGLES) 82 83 85 39: 158 type=133 (ANGLES) 84 83 85 39: 159 type=133 (ANGLES) 82 86 87 39: 160 type=133 (ANGLES) 82 86 88 39: 161 type=133 (ANGLES) 87 86 88 39: 162 type=122 (ANGLES) 69 89 90 39: 163 type=123 (ANGLES) 69 89 91 39: 164 type=124 (ANGLES) 90 89 91 39: 165 type=125 (ANGLES) 89 91 92 39: 166 type=126 (ANGLES) 89 91 93 39: 167 type=127 (ANGLES) 92 91 93 39: 168 type=116 (ANGLES) 91 93 94 39: 169 type=128 (ANGLES) 91 93 95 39: 170 type=129 (ANGLES) 91 93 100 39: 171 type=118 (ANGLES) 94 93 95 39: 172 type=116 (ANGLES) 94 93 100 39: 173 type=119 (ANGLES) 95 93 100 39: 174 type=118 (ANGLES) 93 95 96 39: 175 type=118 (ANGLES) 93 95 97 39: 176 type=136 (ANGLES) 93 95 98 39: 177 type=121 (ANGLES) 96 95 97 39: 178 type=116 (ANGLES) 96 95 98 39: 179 type=116 (ANGLES) 97 95 98 39: 180 type=137 (ANGLES) 95 98 99 39: 181 type=122 (ANGLES) 93 100 101 39: 182 type=123 (ANGLES) 93 100 102 39: 183 type=124 (ANGLES) 101 100 102 39: 184 type=125 (ANGLES) 100 102 103 39: 185 type=126 (ANGLES) 100 102 104 39: 186 type=127 (ANGLES) 103 102 104 39: 187 type=116 (ANGLES) 102 104 105 39: 188 type=128 (ANGLES) 102 104 106 39: 189 type=129 (ANGLES) 102 104 115 39: 190 type=118 (ANGLES) 105 104 106 39: 191 type=116 (ANGLES) 105 104 115 39: 192 type=119 (ANGLES) 106 104 115 39: 193 type=118 (ANGLES) 104 106 107 39: 194 type=118 (ANGLES) 104 106 108 39: 195 type=120 (ANGLES) 104 106 109 39: 196 type=121 (ANGLES) 107 106 108 39: 197 type=118 (ANGLES) 107 106 109 39: 198 type=118 (ANGLES) 108 106 109 39: 199 type=118 (ANGLES) 106 109 110 39: 200 type=118 (ANGLES) 106 109 111 39: 201 type=119 (ANGLES) 106 109 112 39: 202 type=121 (ANGLES) 110 109 111 39: 203 type=116 (ANGLES) 110 109 112 39: 204 type=116 (ANGLES) 111 109 112 39: 205 type=138 (ANGLES) 109 112 113 39: 206 type=138 (ANGLES) 109 112 114 39: 207 type=139 (ANGLES) 113 112 114 39: 208 type=122 (ANGLES) 104 115 116 39: 209 type=123 (ANGLES) 104 115 117 39: 210 type=124 (ANGLES) 116 115 117 39: 211 type=125 (ANGLES) 115 117 118 39: 212 type=126 (ANGLES) 115 117 119 39: 213 type=127 (ANGLES) 118 117 119 39: 214 type=116 (ANGLES) 117 119 120 39: 215 type=128 (ANGLES) 117 119 121 39: 216 type=129 (ANGLES) 117 119 134 39: 217 type=118 (ANGLES) 120 119 121 39: 218 type=116 (ANGLES) 120 119 134 39: 219 type=119 (ANGLES) 121 119 134 39: 220 type=118 (ANGLES) 119 121 122 39: 221 type=118 (ANGLES) 119 121 123 39: 222 type=120 (ANGLES) 119 121 124 39: 223 type=121 (ANGLES) 122 121 123 39: 224 type=118 (ANGLES) 122 121 124 39: 225 type=118 (ANGLES) 123 121 124 39: 226 type=118 (ANGLES) 121 124 125 39: 227 type=120 (ANGLES) 121 124 126 39: 228 type=120 (ANGLES) 121 124 130 39: 229 type=118 (ANGLES) 125 124 126 39: 230 type=118 (ANGLES) 125 124 130 39: 231 type=120 (ANGLES) 126 124 130 39: 232 type=118 (ANGLES) 124 126 127 39: 233 type=118 (ANGLES) 124 126 128 39: 234 type=118 (ANGLES) 124 126 129 39: 235 type=121 (ANGLES) 127 126 128 39: 236 type=121 (ANGLES) 127 126 129 39: 237 type=121 (ANGLES) 128 126 129 39: 238 type=118 (ANGLES) 124 130 131 39: 239 type=118 (ANGLES) 124 130 132 39: 240 type=118 (ANGLES) 124 130 133 39: 241 type=121 (ANGLES) 131 130 132 39: 242 type=121 (ANGLES) 131 130 133 39: 243 type=121 (ANGLES) 132 130 133 39: 244 type=122 (ANGLES) 119 134 135 39: 245 type=123 (ANGLES) 119 134 136 39: 246 type=124 (ANGLES) 135 134 136 39: 247 type=125 (ANGLES) 134 136 137 39: 248 type=126 (ANGLES) 134 136 138 39: 249 type=127 (ANGLES) 137 136 138 39: 250 type=116 (ANGLES) 136 138 139 39: 251 type=128 (ANGLES) 136 138 140 39: 252 type=129 (ANGLES) 136 138 144 39: 253 type=118 (ANGLES) 139 138 140 39: 254 type=116 (ANGLES) 139 138 144 39: 255 type=119 (ANGLES) 140 138 144 39: 256 type=118 (ANGLES) 138 140 141 39: 257 type=118 (ANGLES) 138 140 142 39: 258 type=118 (ANGLES) 138 140 143 39: 259 type=121 (ANGLES) 141 140 142 39: 260 type=121 (ANGLES) 141 140 143 39: 261 type=121 (ANGLES) 142 140 143 39: 262 type=122 (ANGLES) 138 144 145 39: 263 type=123 (ANGLES) 138 144 146 39: 264 type=124 (ANGLES) 145 144 146 39: 265 type=125 (ANGLES) 144 146 147 39: 266 type=126 (ANGLES) 144 146 148 39: 267 type=127 (ANGLES) 147 146 148 39: 268 type=116 (ANGLES) 146 148 149 39: 269 type=128 (ANGLES) 146 148 150 39: 270 type=129 (ANGLES) 146 148 154 39: 271 type=118 (ANGLES) 149 148 150 39: 272 type=116 (ANGLES) 149 148 154 39: 273 type=119 (ANGLES) 150 148 154 39: 274 type=118 (ANGLES) 148 150 151 39: 275 type=118 (ANGLES) 148 150 152 39: 276 type=118 (ANGLES) 148 150 153 39: 277 type=121 (ANGLES) 151 150 152 39: 278 type=121 (ANGLES) 151 150 153 39: 279 type=121 (ANGLES) 152 150 153 39: 280 type=122 (ANGLES) 148 154 155 39: G96Angle: 39: nr: 0 39: Restricted Angles: 39: nr: 0 39: Lin. Angle: 39: nr: 0 39: Bond-Cross: 39: nr: 0 39: BA-Cross: 39: nr: 0 39: U-B: 39: nr: 0 39: Quartic Angles: 39: nr: 0 39: Tab. Angles: 39: nr: 0 39: Proper Dih.: 39: nr: 145 39: iatoms: 39: 0 type=140 (PDIHS) 4 24 22 23 39: 1 type=141 (PDIHS) 22 26 24 25 39: 2 type=140 (PDIHS) 26 40 38 39 39: 3 type=141 (PDIHS) 38 42 40 41 39: 4 type=140 (PDIHS) 42 60 58 59 39: 5 type=142 (PDIHS) 44 47 50 48 39: 6 type=142 (PDIHS) 47 52 48 49 39: 7 type=142 (PDIHS) 47 54 50 51 39: 8 type=142 (PDIHS) 48 56 52 53 39: 9 type=142 (PDIHS) 50 56 54 55 39: 10 type=142 (PDIHS) 52 54 56 57 39: 11 type=141 (PDIHS) 58 62 60 61 39: 12 type=140 (PDIHS) 62 67 65 66 39: 13 type=141 (PDIHS) 65 69 67 68 39: 14 type=140 (PDIHS) 69 91 89 90 39: 15 type=141 (PDIHS) 77 82 80 81 39: 16 type=140 (PDIHS) 80 83 82 86 39: 17 type=141 (PDIHS) 82 84 83 85 39: 18 type=141 (PDIHS) 82 87 86 88 39: 19 type=141 (PDIHS) 89 93 91 92 39: 20 type=140 (PDIHS) 93 102 100 101 39: 21 type=141 (PDIHS) 100 104 102 103 39: 22 type=140 (PDIHS) 104 117 115 116 39: 23 type=140 (PDIHS) 109 113 112 114 39: 24 type=141 (PDIHS) 115 119 117 118 39: 25 type=140 (PDIHS) 119 136 134 135 39: 26 type=141 (PDIHS) 134 138 136 137 39: 27 type=140 (PDIHS) 138 146 144 145 39: 28 type=141 (PDIHS) 144 148 146 147 39: Ryckaert-Bell.: 39: nr: 1565 39: iatoms: 39: 0 type=143 (RBDIHS) 1 0 4 5 39: 1 type=144 (RBDIHS) 1 0 4 6 39: 2 type=144 (RBDIHS) 1 0 4 22 39: 3 type=143 (RBDIHS) 2 0 4 5 39: 4 type=144 (RBDIHS) 2 0 4 6 39: 5 type=144 (RBDIHS) 2 0 4 22 39: 6 type=143 (RBDIHS) 3 0 4 5 39: 7 type=144 (RBDIHS) 3 0 4 6 39: 8 type=144 (RBDIHS) 3 0 4 22 39: 9 type=145 (RBDIHS) 0 4 6 9 39: 10 type=146 (RBDIHS) 22 4 6 9 39: 11 type=147 (RBDIHS) 0 4 6 7 39: 12 type=147 (RBDIHS) 0 4 6 8 39: 13 type=148 (RBDIHS) 5 4 6 7 39: 14 type=148 (RBDIHS) 5 4 6 8 39: 15 type=148 (RBDIHS) 5 4 6 9 39: 16 type=149 (RBDIHS) 22 4 6 7 39: 17 type=149 (RBDIHS) 22 4 6 8 39: 18 type=150 (RBDIHS) 0 4 22 24 39: 19 type=151 (RBDIHS) 6 4 22 24 39: 20 type=148 (RBDIHS) 4 6 9 10 39: 21 type=148 (RBDIHS) 4 6 9 11 39: 22 type=152 (RBDIHS) 4 6 9 12 39: 23 type=148 (RBDIHS) 7 6 9 10 39: 24 type=148 (RBDIHS) 7 6 9 11 39: 25 type=148 (RBDIHS) 7 6 9 12 39: 26 type=148 (RBDIHS) 8 6 9 10 39: 27 type=148 (RBDIHS) 8 6 9 11 39: 28 type=148 (RBDIHS) 8 6 9 12 39: 29 type=148 (RBDIHS) 6 9 12 13 39: 30 type=148 (RBDIHS) 6 9 12 14 39: 31 type=152 (RBDIHS) 6 9 12 15 39: 32 type=148 (RBDIHS) 10 9 12 13 39: 33 type=148 (RBDIHS) 10 9 12 14 39: 34 type=148 (RBDIHS) 10 9 12 15 39: 35 type=148 (RBDIHS) 11 9 12 13 39: 36 type=148 (RBDIHS) 11 9 12 14 39: 37 type=148 (RBDIHS) 11 9 12 15 39: 38 type=148 (RBDIHS) 9 12 15 16 39: 39 type=148 (RBDIHS) 9 12 15 17 39: 40 type=153 (RBDIHS) 9 12 15 18 39: 41 type=148 (RBDIHS) 13 12 15 16 39: 42 type=148 (RBDIHS) 13 12 15 17 39: 43 type=154 (RBDIHS) 13 12 15 18 39: 44 type=148 (RBDIHS) 14 12 15 16 39: 45 type=148 (RBDIHS) 14 12 15 17 39: 46 type=154 (RBDIHS) 14 12 15 18 39: 47 type=144 (RBDIHS) 12 15 18 19 39: 48 type=144 (RBDIHS) 12 15 18 20 39: 49 type=144 (RBDIHS) 12 15 18 21 39: 50 type=143 (RBDIHS) 16 15 18 19 39: 51 type=143 (RBDIHS) 16 15 18 20 39: 52 type=143 (RBDIHS) 16 15 18 21 39: 53 type=143 (RBDIHS) 17 15 18 19 39: 54 type=143 (RBDIHS) 17 15 18 20 39: 55 type=143 (RBDIHS) 17 15 18 21 39: 56 type=155 (RBDIHS) 4 22 24 25 39: 57 type=156 (RBDIHS) 4 22 24 26 39: 58 type=155 (RBDIHS) 23 22 24 25 39: 59 type=157 (RBDIHS) 23 22 24 26 39: 60 type=158 (RBDIHS) 22 24 26 28 39: 61 type=159 (RBDIHS) 22 24 26 38 39: 62 type=160 (RBDIHS) 24 26 28 30 39: 63 type=160 (RBDIHS) 24 26 28 34 39: 64 type=161 (RBDIHS) 38 26 28 30 39: 65 type=161 (RBDIHS) 38 26 28 34 39: 66 type=147 (RBDIHS) 24 26 28 29 39: 67 type=148 (RBDIHS) 27 26 28 29 39: 68 type=148 (RBDIHS) 27 26 28 30 39: 69 type=148 (RBDIHS) 27 26 28 34 39: 70 type=149 (RBDIHS) 38 26 28 29 39: 71 type=150 (RBDIHS) 24 26 38 40 39: 72 type=151 (RBDIHS) 28 26 38 40 39: 73 type=148 (RBDIHS) 26 28 30 31 39: 74 type=148 (RBDIHS) 26 28 30 32 39: 75 type=148 (RBDIHS) 26 28 30 33 39: 76 type=148 (RBDIHS) 29 28 30 31 39: 77 type=148 (RBDIHS) 29 28 30 32 39: 78 type=148 (RBDIHS) 29 28 30 33 39: 79 type=148 (RBDIHS) 34 28 30 31 39: 80 type=148 (RBDIHS) 34 28 30 32 39: 81 type=148 (RBDIHS) 34 28 30 33 39: 82 type=148 (RBDIHS) 26 28 34 35 39: 83 type=148 (RBDIHS) 26 28 34 36 39: 84 type=148 (RBDIHS) 26 28 34 37 39: 85 type=148 (RBDIHS) 29 28 34 35 39: 86 type=148 (RBDIHS) 29 28 34 36 39: 87 type=148 (RBDIHS) 29 28 34 37 39: 88 type=148 (RBDIHS) 30 28 34 35 39: 89 type=148 (RBDIHS) 30 28 34 36 39: 90 type=148 (RBDIHS) 30 28 34 37 39: 91 type=155 (RBDIHS) 26 38 40 41 39: 92 type=156 (RBDIHS) 26 38 40 42 39: 93 type=155 (RBDIHS) 39 38 40 41 39: 94 type=157 (RBDIHS) 39 38 40 42 39: 95 type=158 (RBDIHS) 38 40 42 44 39: 96 type=159 (RBDIHS) 38 40 42 58 39: 97 type=147 (RBDIHS) 40 42 44 45 39: 98 type=147 (RBDIHS) 40 42 44 46 39: 99 type=162 (RBDIHS) 40 42 44 47 39: 100 type=148 (RBDIHS) 43 42 44 45 39: 101 type=148 (RBDIHS) 43 42 44 46 39: 102 type=163 (RBDIHS) 43 42 44 47 39: 103 type=149 (RBDIHS) 58 42 44 45 39: 104 type=149 (RBDIHS) 58 42 44 46 39: 105 type=164 (RBDIHS) 58 42 44 47 39: 106 type=150 (RBDIHS) 40 42 58 60 39: 107 type=151 (RBDIHS) 44 42 58 60 39: 108 type=165 (RBDIHS) 44 47 48 49 39: 109 type=165 (RBDIHS) 44 47 48 52 39: 110 type=165 (RBDIHS) 50 47 48 49 39: 111 type=165 (RBDIHS) 50 47 48 52 39: 112 type=165 (RBDIHS) 44 47 50 51 39: 113 type=165 (RBDIHS) 44 47 50 54 39: 114 type=165 (RBDIHS) 48 47 50 51 39: 115 type=165 (RBDIHS) 48 47 50 54 39: 116 type=165 (RBDIHS) 47 48 52 53 39: 117 type=165 (RBDIHS) 47 48 52 56 39: 118 type=165 (RBDIHS) 49 48 52 53 39: 119 type=165 (RBDIHS) 49 48 52 56 39: 120 type=165 (RBDIHS) 47 50 54 55 39: 121 type=165 (RBDIHS) 47 50 54 56 39: 122 type=165 (RBDIHS) 51 50 54 55 39: 123 type=165 (RBDIHS) 51 50 54 56 39: 124 type=165 (RBDIHS) 48 52 56 54 39: 125 type=165 (RBDIHS) 48 52 56 57 39: 126 type=165 (RBDIHS) 53 52 56 54 39: 127 type=165 (RBDIHS) 53 52 56 57 39: 128 type=165 (RBDIHS) 50 54 56 52 39: 129 type=165 (RBDIHS) 50 54 56 57 39: 130 type=165 (RBDIHS) 55 54 56 52 39: 131 type=165 (RBDIHS) 55 54 56 57 39: 132 type=155 (RBDIHS) 42 58 60 61 39: 133 type=156 (RBDIHS) 42 58 60 62 39: 134 type=155 (RBDIHS) 59 58 60 61 39: 135 type=157 (RBDIHS) 59 58 60 62 39: 136 type=159 (RBDIHS) 58 60 62 65 39: 137 type=150 (RBDIHS) 60 62 65 67 39: 138 type=155 (RBDIHS) 62 65 67 68 39: 139 type=156 (RBDIHS) 62 65 67 69 39: 140 type=155 (RBDIHS) 66 65 67 68 39: 141 type=157 (RBDIHS) 66 65 67 69 39: 142 type=158 (RBDIHS) 65 67 69 71 39: 143 type=159 (RBDIHS) 65 67 69 89 39: 144 type=166 (RBDIHS) 67 69 71 74 39: 145 type=167 (RBDIHS) 89 69 71 74 39: 146 type=147 (RBDIHS) 67 69 71 72 39: 147 type=147 (RBDIHS) 67 69 71 73 39: 148 type=148 (RBDIHS) 70 69 71 72 39: 149 type=148 (RBDIHS) 70 69 71 73 39: 150 type=148 (RBDIHS) 70 69 71 74 39: 151 type=149 (RBDIHS) 89 69 71 72 39: 152 type=149 (RBDIHS) 89 69 71 73 39: 153 type=150 (RBDIHS) 67 69 89 91 39: 154 type=151 (RBDIHS) 71 69 89 91 39: 155 type=148 (RBDIHS) 69 71 74 75 39: 156 type=148 (RBDIHS) 69 71 74 76 39: 157 type=152 (RBDIHS) 69 71 74 77 39: 158 type=148 (RBDIHS) 72 71 74 75 39: 159 type=148 (RBDIHS) 72 71 74 76 39: 160 type=148 (RBDIHS) 72 71 74 77 39: 161 type=148 (RBDIHS) 73 71 74 75 39: 162 type=148 (RBDIHS) 73 71 74 76 39: 163 type=148 (RBDIHS) 73 71 74 77 39: 164 type=148 (RBDIHS) 71 74 77 78 39: 165 type=148 (RBDIHS) 71 74 77 79 39: 166 type=153 (RBDIHS) 71 74 77 80 39: 167 type=148 (RBDIHS) 75 74 77 78 39: 168 type=148 (RBDIHS) 75 74 77 79 39: 169 type=168 (RBDIHS) 75 74 77 80 39: 170 type=148 (RBDIHS) 76 74 77 78 39: 171 type=148 (RBDIHS) 76 74 77 79 39: 172 type=168 (RBDIHS) 76 74 77 80 39: 173 type=169 (RBDIHS) 74 77 80 81 39: 174 type=170 (RBDIHS) 74 77 80 82 39: 175 type=171 (RBDIHS) 78 77 80 82 39: 176 type=171 (RBDIHS) 79 77 80 82 39: 177 type=172 (RBDIHS) 77 80 82 83 39: 178 type=172 (RBDIHS) 77 80 82 86 39: 179 type=173 (RBDIHS) 81 80 82 83 39: 180 type=173 (RBDIHS) 81 80 82 86 39: 181 type=173 (RBDIHS) 80 82 83 84 39: 182 type=173 (RBDIHS) 80 82 83 85 39: 183 type=173 (RBDIHS) 86 82 83 84 39: 184 type=173 (RBDIHS) 86 82 83 85 39: 185 type=173 (RBDIHS) 80 82 86 87 39: 186 type=173 (RBDIHS) 80 82 86 88 39: 187 type=173 (RBDIHS) 83 82 86 87 39: 188 type=173 (RBDIHS) 83 82 86 88 39: 189 type=155 (RBDIHS) 69 89 91 92 39: 190 type=156 (RBDIHS) 69 89 91 93 39: 191 type=155 (RBDIHS) 90 89 91 92 39: 192 type=157 (RBDIHS) 90 89 91 93 39: 193 type=158 (RBDIHS) 89 91 93 95 39: 194 type=159 (RBDIHS) 89 91 93 100 39: 195 type=174 (RBDIHS) 91 93 95 98 39: 196 type=175 (RBDIHS) 100 93 95 98 39: 197 type=147 (RBDIHS) 91 93 95 96 39: 198 type=147 (RBDIHS) 91 93 95 97 39: 199 type=148 (RBDIHS) 94 93 95 96 39: 200 type=148 (RBDIHS) 94 93 95 97 39: 201 type=176 (RBDIHS) 94 93 95 98 39: 202 type=149 (RBDIHS) 100 93 95 96 39: 203 type=149 (RBDIHS) 100 93 95 97 39: 204 type=150 (RBDIHS) 91 93 100 102 39: 205 type=151 (RBDIHS) 95 93 100 102 39: 206 type=177 (RBDIHS) 93 95 98 99 39: 207 type=178 (RBDIHS) 96 95 98 99 39: 208 type=178 (RBDIHS) 97 95 98 99 39: 209 type=155 (RBDIHS) 93 100 102 103 39: 210 type=156 (RBDIHS) 93 100 102 104 39: 211 type=155 (RBDIHS) 101 100 102 103 39: 212 type=157 (RBDIHS) 101 100 102 104 39: 213 type=158 (RBDIHS) 100 102 104 106 39: 214 type=159 (RBDIHS) 100 102 104 115 39: 215 type=179 (RBDIHS) 102 104 106 109 39: 216 type=180 (RBDIHS) 115 104 106 109 39: 217 type=147 (RBDIHS) 102 104 106 107 39: 218 type=147 (RBDIHS) 102 104 106 108 39: 219 type=148 (RBDIHS) 105 104 106 107 39: 220 type=148 (RBDIHS) 105 104 106 108 39: 221 type=148 (RBDIHS) 105 104 106 109 39: 222 type=149 (RBDIHS) 115 104 106 107 39: 223 type=149 (RBDIHS) 115 104 106 108 39: 224 type=150 (RBDIHS) 102 104 115 117 39: 225 type=151 (RBDIHS) 106 104 115 117 39: 226 type=148 (RBDIHS) 104 106 109 110 39: 227 type=148 (RBDIHS) 104 106 109 111 39: 228 type=181 (RBDIHS) 104 106 109 112 39: 229 type=148 (RBDIHS) 107 106 109 110 39: 230 type=148 (RBDIHS) 107 106 109 111 39: 231 type=182 (RBDIHS) 107 106 109 112 39: 232 type=148 (RBDIHS) 108 106 109 110 39: 233 type=148 (RBDIHS) 108 106 109 111 39: 234 type=182 (RBDIHS) 108 106 109 112 39: 235 type=183 (RBDIHS) 106 109 112 113 39: 236 type=183 (RBDIHS) 106 109 112 114 39: 237 type=155 (RBDIHS) 104 115 117 118 39: 238 type=156 (RBDIHS) 104 115 117 119 39: 239 type=155 (RBDIHS) 116 115 117 118 39: 240 type=157 (RBDIHS) 116 115 117 119 39: 241 type=158 (RBDIHS) 115 117 119 121 39: 242 type=159 (RBDIHS) 115 117 119 134 39: 243 type=184 (RBDIHS) 117 119 121 124 39: 244 type=185 (RBDIHS) 134 119 121 124 39: 245 type=147 (RBDIHS) 117 119 121 122 39: 246 type=147 (RBDIHS) 117 119 121 123 39: 247 type=148 (RBDIHS) 120 119 121 122 39: 248 type=148 (RBDIHS) 120 119 121 123 39: 249 type=148 (RBDIHS) 120 119 121 124 39: 250 type=149 (RBDIHS) 134 119 121 122 39: 251 type=149 (RBDIHS) 134 119 121 123 39: 252 type=150 (RBDIHS) 117 119 134 136 39: 253 type=151 (RBDIHS) 121 119 134 136 39: 254 type=148 (RBDIHS) 119 121 124 125 39: 255 type=152 (RBDIHS) 119 121 124 126 39: 256 type=152 (RBDIHS) 119 121 124 130 39: 257 type=148 (RBDIHS) 122 121 124 125 39: 258 type=148 (RBDIHS) 122 121 124 126 39: 259 type=148 (RBDIHS) 122 121 124 130 39: 260 type=148 (RBDIHS) 123 121 124 125 39: 261 type=148 (RBDIHS) 123 121 124 126 39: 262 type=148 (RBDIHS) 123 121 124 130 39: 263 type=148 (RBDIHS) 121 124 126 127 39: 264 type=148 (RBDIHS) 121 124 126 128 39: 265 type=148 (RBDIHS) 121 124 126 129 39: 266 type=148 (RBDIHS) 125 124 126 127 39: 267 type=148 (RBDIHS) 125 124 126 128 39: 268 type=148 (RBDIHS) 125 124 126 129 39: 269 type=148 (RBDIHS) 130 124 126 127 39: 270 type=148 (RBDIHS) 130 124 126 128 39: 271 type=148 (RBDIHS) 130 124 126 129 39: 272 type=148 (RBDIHS) 121 124 130 131 39: 273 type=148 (RBDIHS) 121 124 130 132 39: 274 type=148 (RBDIHS) 121 124 130 133 39: 275 type=148 (RBDIHS) 125 124 130 131 39: 276 type=148 (RBDIHS) 125 124 130 132 39: 277 type=148 (RBDIHS) 125 124 130 133 39: 278 type=148 (RBDIHS) 126 124 130 131 39: 279 type=148 (RBDIHS) 126 124 130 132 39: 280 type=148 (RBDIHS) 126 124 130 133 39: 281 type=155 (RBDIHS) 119 134 136 137 39: 282 type=156 (RBDIHS) 119 134 136 138 39: 283 type=155 (RBDIHS) 135 134 136 137 39: 284 type=157 (RBDIHS) 135 134 136 138 39: 285 type=158 (RBDIHS) 134 136 138 140 39: 286 type=159 (RBDIHS) 134 136 138 144 39: 287 type=147 (RBDIHS) 136 138 140 141 39: 288 type=147 (RBDIHS) 136 138 140 142 39: 289 type=147 (RBDIHS) 136 138 140 143 39: 290 type=148 (RBDIHS) 139 138 140 141 39: 291 type=148 (RBDIHS) 139 138 140 142 39: 292 type=148 (RBDIHS) 139 138 140 143 39: 293 type=149 (RBDIHS) 144 138 140 141 39: 294 type=149 (RBDIHS) 144 138 140 142 39: 295 type=149 (RBDIHS) 144 138 140 143 39: 296 type=150 (RBDIHS) 136 138 144 146 39: 297 type=151 (RBDIHS) 140 138 144 146 39: 298 type=155 (RBDIHS) 138 144 146 147 39: 299 type=156 (RBDIHS) 138 144 146 148 39: 300 type=155 (RBDIHS) 145 144 146 147 39: 301 type=157 (RBDIHS) 145 144 146 148 39: 302 type=158 (RBDIHS) 144 146 148 150 39: 303 type=159 (RBDIHS) 144 146 148 154 39: 304 type=147 (RBDIHS) 146 148 150 151 39: 305 type=147 (RBDIHS) 146 148 150 152 39: 306 type=147 (RBDIHS) 146 148 150 153 39: 307 type=148 (RBDIHS) 149 148 150 151 39: 308 type=148 (RBDIHS) 149 148 150 152 39: 309 type=148 (RBDIHS) 149 148 150 153 39: 310 type=149 (RBDIHS) 154 148 150 151 39: 311 type=149 (RBDIHS) 154 148 150 152 39: 312 type=149 (RBDIHS) 154 148 150 153 39: Restricted Dih.: 39: nr: 0 39: CBT Dih.: 39: nr: 0 39: Fourier Dih.: 39: nr: 0 39: Improper Dih.: 39: nr: 0 39: Improper Dih.: 39: nr: 0 39: Tab. Dih.: 39: nr: 0 39: CMAP Dih.: 39: nr: 0 39: GB 1-2 Pol. (unused): 39: nr: 0 39: GB 1-3 Pol. (unused): 39: nr: 0 39: GB 1-4 Pol. (unused): 39: nr: 0 39: GB Polarization (unused): 39: nr: 0 39: Nonpolar Sol. (unused): 39: nr: 0 39: LJ-14: 39: nr: 1197 39: iatoms: 39: 0 type=186 (LJ14) 0 7 39: 1 type=186 (LJ14) 0 8 39: 2 type=187 (LJ14) 0 9 39: 3 type=188 (LJ14) 0 23 39: 4 type=189 (LJ14) 0 24 39: 5 type=190 (LJ14) 1 5 39: 6 type=190 (LJ14) 1 6 39: 7 type=190 (LJ14) 1 22 39: 8 type=190 (LJ14) 2 5 39: 9 type=190 (LJ14) 2 6 39: 10 type=190 (LJ14) 2 22 39: 11 type=190 (LJ14) 3 5 39: 12 type=190 (LJ14) 3 6 39: 13 type=190 (LJ14) 3 22 39: 14 type=191 (LJ14) 4 10 39: 15 type=191 (LJ14) 4 11 39: 16 type=192 (LJ14) 4 12 39: 17 type=190 (LJ14) 4 25 39: 18 type=192 (LJ14) 4 26 39: 19 type=193 (LJ14) 5 7 39: 20 type=193 (LJ14) 5 8 39: 21 type=191 (LJ14) 5 9 39: 22 type=194 (LJ14) 5 23 39: 23 type=186 (LJ14) 5 24 39: 24 type=191 (LJ14) 6 13 39: 25 type=191 (LJ14) 6 14 39: 26 type=192 (LJ14) 6 15 39: 27 type=195 (LJ14) 6 23 39: 28 type=187 (LJ14) 6 24 39: 29 type=193 (LJ14) 7 10 39: 30 type=193 (LJ14) 7 11 39: 31 type=191 (LJ14) 7 12 39: 32 type=196 (LJ14) 7 22 39: 33 type=193 (LJ14) 8 10 39: 34 type=193 (LJ14) 8 11 39: 35 type=191 (LJ14) 8 12 39: 36 type=196 (LJ14) 8 22 39: 37 type=191 (LJ14) 9 16 39: 38 type=191 (LJ14) 9 17 39: 39 type=187 (LJ14) 9 18 39: 40 type=197 (LJ14) 9 22 39: 41 type=193 (LJ14) 10 13 39: 42 type=193 (LJ14) 10 14 39: 43 type=191 (LJ14) 10 15 39: 44 type=193 (LJ14) 11 13 39: 45 type=193 (LJ14) 11 14 39: 46 type=191 (LJ14) 11 15 39: 47 type=190 (LJ14) 12 19 39: 48 type=190 (LJ14) 12 20 39: 49 type=190 (LJ14) 12 21 39: 50 type=193 (LJ14) 13 16 39: 51 type=193 (LJ14) 13 17 39: 52 type=186 (LJ14) 13 18 39: 53 type=193 (LJ14) 14 16 39: 54 type=193 (LJ14) 14 17 39: 55 type=186 (LJ14) 14 18 39: 56 type=190 (LJ14) 16 19 39: 57 type=190 (LJ14) 16 20 39: 58 type=190 (LJ14) 16 21 39: 59 type=190 (LJ14) 17 19 39: 60 type=190 (LJ14) 17 20 39: 61 type=190 (LJ14) 17 21 39: 62 type=196 (LJ14) 22 27 39: 63 type=197 (LJ14) 22 28 39: 64 type=198 (LJ14) 22 38 39: 65 type=190 (LJ14) 23 25 39: 66 type=195 (LJ14) 23 26 39: 67 type=186 (LJ14) 24 29 39: 68 type=187 (LJ14) 24 30 39: 69 type=187 (LJ14) 24 34 39: 70 type=188 (LJ14) 24 39 39: 71 type=189 (LJ14) 24 40 39: 72 type=190 (LJ14) 25 27 39: 73 type=190 (LJ14) 25 28 39: 74 type=190 (LJ14) 25 38 39: 75 type=191 (LJ14) 26 31 39: 76 type=191 (LJ14) 26 32 39: 77 type=191 (LJ14) 26 33 39: 78 type=191 (LJ14) 26 35 39: 79 type=191 (LJ14) 26 36 39: 80 type=191 (LJ14) 26 37 39: 81 type=190 (LJ14) 26 41 39: 82 type=192 (LJ14) 26 42 39: 83 type=193 (LJ14) 27 29 39: 84 type=191 (LJ14) 27 30 39: 85 type=191 (LJ14) 27 34 39: 86 type=194 (LJ14) 27 39 39: 87 type=186 (LJ14) 27 40 39: 88 type=195 (LJ14) 28 39 39: 89 type=187 (LJ14) 28 40 39: 90 type=193 (LJ14) 29 31 39: 91 type=193 (LJ14) 29 32 39: 92 type=193 (LJ14) 29 33 39: 93 type=193 (LJ14) 29 35 39: 94 type=193 (LJ14) 29 36 39: 95 type=193 (LJ14) 29 37 39: 96 type=196 (LJ14) 29 38 39: 97 type=191 (LJ14) 30 35 39: 98 type=191 (LJ14) 30 36 39: 99 type=191 (LJ14) 30 37 39: 100 type=197 (LJ14) 30 38 39: 101 type=191 (LJ14) 31 34 39: 102 type=191 (LJ14) 32 34 39: 103 type=191 (LJ14) 33 34 39: 104 type=197 (LJ14) 34 38 39: 105 type=196 (LJ14) 38 43 39: 106 type=197 (LJ14) 38 44 39: 107 type=198 (LJ14) 38 58 39: 108 type=190 (LJ14) 39 41 39: 109 type=195 (LJ14) 39 42 39: 110 type=186 (LJ14) 40 45 39: 111 type=186 (LJ14) 40 46 39: 112 type=199 (LJ14) 40 47 39: 113 type=188 (LJ14) 40 59 39: 114 type=189 (LJ14) 40 60 39: 115 type=190 (LJ14) 41 43 39: 116 type=190 (LJ14) 41 44 39: 117 type=190 (LJ14) 41 58 39: 118 type=200 (LJ14) 42 48 39: 119 type=200 (LJ14) 42 50 39: 120 type=190 (LJ14) 42 61 39: 121 type=192 (LJ14) 42 62 39: 122 type=193 (LJ14) 43 45 39: 123 type=193 (LJ14) 43 46 39: 124 type=201 (LJ14) 43 47 39: 125 type=194 (LJ14) 43 59 39: 126 type=186 (LJ14) 43 60 39: 127 type=202 (LJ14) 44 49 39: 128 type=202 (LJ14) 44 51 39: 129 type=200 (LJ14) 44 52 39: 130 type=200 (LJ14) 44 54 39: 131 type=195 (LJ14) 44 59 39: 132 type=187 (LJ14) 44 60 39: 133 type=201 (LJ14) 45 48 39: 134 type=201 (LJ14) 45 50 39: 135 type=196 (LJ14) 45 58 39: 136 type=201 (LJ14) 46 48 39: 137 type=201 (LJ14) 46 50 39: 138 type=196 (LJ14) 46 58 39: 139 type=203 (LJ14) 47 53 39: 140 type=203 (LJ14) 47 55 39: 141 type=204 (LJ14) 47 56 39: 142 type=205 (LJ14) 47 58 39: 143 type=203 (LJ14) 48 51 39: 144 type=204 (LJ14) 48 54 39: 145 type=203 (LJ14) 48 57 39: 146 type=203 (LJ14) 49 50 39: 147 type=206 (LJ14) 49 53 39: 148 type=203 (LJ14) 49 56 39: 149 type=204 (LJ14) 50 52 39: 150 type=203 (LJ14) 50 57 39: 151 type=206 (LJ14) 51 55 39: 152 type=203 (LJ14) 51 56 39: 153 type=203 (LJ14) 52 55 39: 154 type=203 (LJ14) 53 54 39: 155 type=206 (LJ14) 53 57 39: 156 type=206 (LJ14) 55 57 39: 157 type=196 (LJ14) 58 63 39: 158 type=196 (LJ14) 58 64 39: 159 type=198 (LJ14) 58 65 39: 160 type=190 (LJ14) 59 61 39: 161 type=195 (LJ14) 59 62 39: 162 type=188 (LJ14) 60 66 39: 163 type=189 (LJ14) 60 67 39: 164 type=190 (LJ14) 61 63 39: 165 type=190 (LJ14) 61 64 39: 166 type=190 (LJ14) 61 65 39: 167 type=190 (LJ14) 62 68 39: 168 type=192 (LJ14) 62 69 39: 169 type=194 (LJ14) 63 66 39: 170 type=186 (LJ14) 63 67 39: 171 type=194 (LJ14) 64 66 39: 172 type=186 (LJ14) 64 67 39: 173 type=196 (LJ14) 65 70 39: 174 type=197 (LJ14) 65 71 39: 175 type=198 (LJ14) 65 89 39: 176 type=190 (LJ14) 66 68 39: 177 type=195 (LJ14) 66 69 39: 178 type=186 (LJ14) 67 72 39: 179 type=186 (LJ14) 67 73 39: 180 type=187 (LJ14) 67 74 39: 181 type=188 (LJ14) 67 90 39: 182 type=189 (LJ14) 67 91 39: 183 type=190 (LJ14) 68 70 39: 184 type=190 (LJ14) 68 71 39: 185 type=190 (LJ14) 68 89 39: 186 type=191 (LJ14) 69 75 39: 187 type=191 (LJ14) 69 76 39: 188 type=192 (LJ14) 69 77 39: 189 type=190 (LJ14) 69 92 39: 190 type=192 (LJ14) 69 93 39: 191 type=193 (LJ14) 70 72 39: 192 type=193 (LJ14) 70 73 39: 193 type=191 (LJ14) 70 74 39: 194 type=194 (LJ14) 70 90 39: 195 type=186 (LJ14) 70 91 39: 196 type=191 (LJ14) 71 78 39: 197 type=191 (LJ14) 71 79 39: 198 type=187 (LJ14) 71 80 39: 199 type=195 (LJ14) 71 90 39: 200 type=187 (LJ14) 71 91 39: 201 type=193 (LJ14) 72 75 39: 202 type=193 (LJ14) 72 76 39: 203 type=191 (LJ14) 72 77 39: 204 type=196 (LJ14) 72 89 39: 205 type=193 (LJ14) 73 75 39: 206 type=193 (LJ14) 73 76 39: 207 type=191 (LJ14) 73 77 39: 208 type=196 (LJ14) 73 89 39: 209 type=190 (LJ14) 74 81 39: 210 type=207 (LJ14) 74 82 39: 211 type=197 (LJ14) 74 89 39: 212 type=193 (LJ14) 75 78 39: 213 type=193 (LJ14) 75 79 39: 214 type=186 (LJ14) 75 80 39: 215 type=193 (LJ14) 76 78 39: 216 type=193 (LJ14) 76 79 39: 217 type=186 (LJ14) 76 80 39: 218 type=187 (LJ14) 77 83 39: 219 type=187 (LJ14) 77 86 39: 220 type=190 (LJ14) 78 81 39: 221 type=208 (LJ14) 78 82 39: 222 type=190 (LJ14) 79 81 39: 223 type=208 (LJ14) 79 82 39: 224 type=190 (LJ14) 80 84 39: 225 type=190 (LJ14) 80 85 39: 226 type=190 (LJ14) 80 87 39: 227 type=190 (LJ14) 80 88 39: 228 type=190 (LJ14) 81 83 39: 229 type=190 (LJ14) 81 86 39: 230 type=190 (LJ14) 83 87 39: 231 type=190 (LJ14) 83 88 39: 232 type=190 (LJ14) 84 86 39: 233 type=190 (LJ14) 85 86 39: 234 type=196 (LJ14) 89 94 39: 235 type=197 (LJ14) 89 95 39: 236 type=198 (LJ14) 89 100 39: 237 type=190 (LJ14) 90 92 39: 238 type=195 (LJ14) 90 93 39: 239 type=186 (LJ14) 91 96 39: 240 type=186 (LJ14) 91 97 39: 241 type=209 (LJ14) 91 98 39: 242 type=188 (LJ14) 91 101 39: 243 type=189 (LJ14) 91 102 39: 244 type=190 (LJ14) 92 94 39: 245 type=190 (LJ14) 92 95 39: 246 type=190 (LJ14) 92 100 39: 247 type=190 (LJ14) 93 99 39: 248 type=190 (LJ14) 93 103 39: 249 type=192 (LJ14) 93 104 39: 250 type=193 (LJ14) 94 96 39: 251 type=193 (LJ14) 94 97 39: 252 type=210 (LJ14) 94 98 39: 253 type=194 (LJ14) 94 101 39: 254 type=186 (LJ14) 94 102 39: 255 type=195 (LJ14) 95 101 39: 256 type=187 (LJ14) 95 102 39: 257 type=190 (LJ14) 96 99 39: 258 type=196 (LJ14) 96 100 39: 259 type=190 (LJ14) 97 99 39: 260 type=196 (LJ14) 97 100 39: 261 type=211 (LJ14) 98 100 39: 262 type=196 (LJ14) 100 105 39: 263 type=197 (LJ14) 100 106 39: 264 type=198 (LJ14) 100 115 39: 265 type=190 (LJ14) 101 103 39: 266 type=195 (LJ14) 101 104 39: 267 type=186 (LJ14) 102 107 39: 268 type=186 (LJ14) 102 108 39: 269 type=187 (LJ14) 102 109 39: 270 type=188 (LJ14) 102 116 39: 271 type=189 (LJ14) 102 117 39: 272 type=190 (LJ14) 103 105 39: 273 type=190 (LJ14) 103 106 39: 274 type=190 (LJ14) 103 115 39: 275 type=191 (LJ14) 104 110 39: 276 type=191 (LJ14) 104 111 39: 277 type=197 (LJ14) 104 112 39: 278 type=190 (LJ14) 104 118 39: 279 type=192 (LJ14) 104 119 39: 280 type=193 (LJ14) 105 107 39: 281 type=193 (LJ14) 105 108 39: 282 type=191 (LJ14) 105 109 39: 283 type=194 (LJ14) 105 116 39: 284 type=186 (LJ14) 105 117 39: 285 type=195 (LJ14) 106 113 39: 286 type=195 (LJ14) 106 114 39: 287 type=195 (LJ14) 106 116 39: 288 type=187 (LJ14) 106 117 39: 289 type=193 (LJ14) 107 110 39: 290 type=193 (LJ14) 107 111 39: 291 type=196 (LJ14) 107 112 39: 292 type=196 (LJ14) 107 115 39: 293 type=193 (LJ14) 108 110 39: 294 type=193 (LJ14) 108 111 39: 295 type=196 (LJ14) 108 112 39: 296 type=196 (LJ14) 108 115 39: 297 type=197 (LJ14) 109 115 39: 298 type=194 (LJ14) 110 113 39: 299 type=194 (LJ14) 110 114 39: 300 type=194 (LJ14) 111 113 39: 301 type=194 (LJ14) 111 114 39: 302 type=196 (LJ14) 115 120 39: 303 type=197 (LJ14) 115 121 39: 304 type=198 (LJ14) 115 134 39: 305 type=190 (LJ14) 116 118 39: 306 type=195 (LJ14) 116 119 39: 307 type=186 (LJ14) 117 122 39: 308 type=186 (LJ14) 117 123 39: 309 type=187 (LJ14) 117 124 39: 310 type=188 (LJ14) 117 135 39: 311 type=189 (LJ14) 117 136 39: 312 type=190 (LJ14) 118 120 39: 313 type=190 (LJ14) 118 121 39: 314 type=190 (LJ14) 118 134 39: 315 type=191 (LJ14) 119 125 39: 316 type=192 (LJ14) 119 126 39: 317 type=192 (LJ14) 119 130 39: 318 type=190 (LJ14) 119 137 39: 319 type=192 (LJ14) 119 138 39: 320 type=193 (LJ14) 120 122 39: 321 type=193 (LJ14) 120 123 39: 322 type=191 (LJ14) 120 124 39: 323 type=194 (LJ14) 120 135 39: 324 type=186 (LJ14) 120 136 39: 325 type=191 (LJ14) 121 127 39: 326 type=191 (LJ14) 121 128 39: 327 type=191 (LJ14) 121 129 39: 328 type=191 (LJ14) 121 131 39: 329 type=191 (LJ14) 121 132 39: 330 type=191 (LJ14) 121 133 39: 331 type=195 (LJ14) 121 135 39: 332 type=187 (LJ14) 121 136 39: 333 type=193 (LJ14) 122 125 39: 334 type=191 (LJ14) 122 126 39: 335 type=191 (LJ14) 122 130 39: 336 type=196 (LJ14) 122 134 39: 337 type=193 (LJ14) 123 125 39: 338 type=191 (LJ14) 123 126 39: 339 type=191 (LJ14) 123 130 39: 340 type=196 (LJ14) 123 134 39: 341 type=197 (LJ14) 124 134 39: 342 type=193 (LJ14) 125 127 39: 343 type=193 (LJ14) 125 128 39: 344 type=193 (LJ14) 125 129 39: 345 type=193 (LJ14) 125 131 39: 346 type=193 (LJ14) 125 132 39: 347 type=193 (LJ14) 125 133 39: 348 type=191 (LJ14) 126 131 39: 349 type=191 (LJ14) 126 132 39: 350 type=191 (LJ14) 126 133 39: 351 type=191 (LJ14) 127 130 39: 352 type=191 (LJ14) 128 130 39: 353 type=191 (LJ14) 129 130 39: 354 type=196 (LJ14) 134 139 39: 355 type=197 (LJ14) 134 140 39: 356 type=198 (LJ14) 134 144 39: 357 type=190 (LJ14) 135 137 39: 358 type=195 (LJ14) 135 138 39: 359 type=186 (LJ14) 136 141 39: 360 type=186 (LJ14) 136 142 39: 361 type=186 (LJ14) 136 143 39: 362 type=188 (LJ14) 136 145 39: 363 type=189 (LJ14) 136 146 39: 364 type=190 (LJ14) 137 139 39: 365 type=190 (LJ14) 137 140 39: 366 type=190 (LJ14) 137 144 39: 367 type=190 (LJ14) 138 147 39: 368 type=192 (LJ14) 138 148 39: 369 type=193 (LJ14) 139 141 39: 370 type=193 (LJ14) 139 142 39: 371 type=193 (LJ14) 139 143 39: 372 type=194 (LJ14) 139 145 39: 373 type=186 (LJ14) 139 146 39: 374 type=195 (LJ14) 140 145 39: 375 type=187 (LJ14) 140 146 39: 376 type=196 (LJ14) 141 144 39: 377 type=196 (LJ14) 142 144 39: 378 type=196 (LJ14) 143 144 39: 379 type=196 (LJ14) 144 149 39: 380 type=197 (LJ14) 144 150 39: 381 type=198 (LJ14) 144 154 39: 382 type=190 (LJ14) 145 147 39: 383 type=195 (LJ14) 145 148 39: 384 type=186 (LJ14) 146 151 39: 385 type=186 (LJ14) 146 152 39: 386 type=186 (LJ14) 146 153 39: 387 type=188 (LJ14) 146 155 39: 388 type=190 (LJ14) 147 149 39: 389 type=190 (LJ14) 147 150 39: 390 type=190 (LJ14) 147 154 39: 391 type=193 (LJ14) 149 151 39: 392 type=193 (LJ14) 149 152 39: 393 type=193 (LJ14) 149 153 39: 394 type=194 (LJ14) 149 155 39: 395 type=195 (LJ14) 150 155 39: 396 type=196 (LJ14) 151 154 39: 397 type=196 (LJ14) 152 154 39: 398 type=196 (LJ14) 153 154 39: Coulomb-14: 39: nr: 0 39: LJC-14 q: 39: nr: 0 39: LJC Pairs NB: 39: nr: 0 39: LJ (SR): 39: nr: 0 39: Buck.ham (SR): 39: nr: 0 39: LJ (unused): 39: nr: 0 39: B.ham (unused): 39: nr: 0 39: Disper. corr.: 39: nr: 0 39: Coulomb (SR): 39: nr: 0 39: Coul (unused): 39: nr: 0 39: RF excl.: 39: nr: 0 39: Coul. recip.: 39: nr: 0 39: LJ recip.: 39: nr: 0 39: DPD: 39: nr: 0 39: Polarization: 39: nr: 0 39: Water Pol.: 39: nr: 0 39: Thole Pol.: 39: nr: 0 39: Anharm. Pol.: 39: nr: 0 39: Position Rest.: 39: nr: 0 39: Flat-bottom posres: 39: nr: 0 39: Dis. Rest.: 39: nr: 0 39: D.R.Viol. (nm): 39: nr: 0 39: Orient. Rest.: 39: nr: 0 39: Ori. R. RMSD: 39: nr: 0 39: Angle Rest.: 39: nr: 0 39: Angle Rest. Z: 39: nr: 0 39: Dih. Rest.: 39: nr: 0 39: Dih. Rest. Viol.: 39: nr: 0 39: Constraint: 39: nr: 0 39: Constr. No Conn.: 39: nr: 0 39: Settle: 39: nr: 0 39: Virtual site 2: 39: nr: 0 39: Virtual site 2fd: 39: nr: 0 39: Virtual site 3: 39: nr: 0 39: Virtual site 3fd: 39: nr: 0 39: Virtual site 3fad: 39: nr: 0 39: Virtual site 3out: 39: nr: 0 39: Virtual site 4fd: 39: nr: 0 39: Virtual site 4fdn: 39: nr: 0 39: Virtual site N: 39: nr: 0 39: COM Pull En.: 39: nr: 0 39: Density fitting: 39: nr: 0 39: Quantum En.: 39: nr: 0 39: Potential: 39: nr: 0 39: Kinetic En.: 39: nr: 0 39: Total Energy: 39: nr: 0 39: Conserved En.: 39: nr: 0 39: Temperature: 39: nr: 0 39: Vir. Temp. (not used): 39: nr: 0 39: Pres. DC: 39: nr: 0 39: Pressure: 39: nr: 0 39: dH/dl constr.: 39: nr: 0 39: dVremain/dl: 39: nr: 0 39: dEkin/dl: 39: nr: 0 39: dVcoul/dl: 39: nr: 0 39: dVvdw/dl: 39: nr: 0 39: dVbonded/dl: 39: nr: 0 39: dVrestraint/dl: 39: nr: 0 39: dVtemperature/dl: 39: nr: 0 39: grp[T-Coupling ] nr=1, name=[ rest] 39: grp[Energy Mon. ] nr=1, name=[ rest] 39: grp[Acceleration] nr=1, name=[ rest] 39: grp[Freeze ] nr=1, name=[ rest] 39: grp[User1 ] nr=1, name=[ rest] 39: grp[User2 ] nr=1, name=[ rest] 39: grp[VCM ] nr=1, name=[ rest] 39: grp[Compressed X] nr=1, name=[ rest] 39: grp[Or. Res. Fit] nr=1, name=[ rest] 39: grp[QMMM ] nr=1, name=[ rest] 39: grpname (11): 39: grpname[0]={name="System"} 39: grpname[1]={name="Protein"} 39: grpname[2]={name="Protein-H"} 39: grpname[3]={name="C-alpha"} 39: grpname[4]={name="Backbone"} 39: grpname[5]={name="MainChain"} 39: grpname[6]={name="MainChain+Cb"} 39: grpname[7]={name="MainChain+H"} 39: grpname[8]={name="SideChain"} 39: grpname[9]={name="SideChain-H"} 39: grpname[10]={name="rest"} 39: groups T-Cou Energ Accel Freez User1 User2 VCM Compr Or. R QMMM 39: allocated 0 0 0 0 0 0 0 0 0 0 39: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0 39: box (3x3): 39: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00} 39: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00} 39: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00} 39: box_rel (3x3): 39: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: boxv (3x3): 39: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: pres_prev (3x3): 39: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: svir_prev (3x3): 39: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: fvir_prev (3x3): 39: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: nosehoover_xi: not available 39: x (156x3): 39: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00} 39: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00} 39: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00} 39: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00} 39: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00} 39: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00} 39: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00} 39: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00} 39: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01} 39: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01} 39: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01} 39: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00} 39: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01} 39: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01} 39: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01} 39: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01} 39: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01} 39: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01} 39: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01} 39: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01} 39: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01} 39: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01} 39: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00} 39: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00} 39: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00} 39: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00} 39: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00} 39: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01} 39: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00} 39: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00} 39: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00} 39: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00} 39: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01} 39: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01} 39: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00} 39: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00} 39: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00} 39: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00} 39: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01} 39: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01} 39: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01} 39: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01} 39: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01} 39: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01} 39: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01} 39: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01} 39: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01} 39: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01} 39: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01} 39: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01} 39: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01} 39: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01} 39: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01} 39: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01} 39: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01} 39: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01} 39: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01} 39: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01} 39: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01} 39: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01} 39: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01} 39: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01} 39: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01} 39: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01} 39: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01} 39: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01} 39: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01} 39: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01} 39: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01} 39: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01} 39: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01} 39: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01} 39: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01} 39: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01} 39: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02} 39: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02} 39: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02} 39: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02} 39: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02} 39: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01} 39: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02} 39: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01} 39: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02} 39: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01} 39: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01} 39: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01} 39: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02} 39: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01} 39: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02} 39: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01} 39: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02} 39: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01} 39: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01} 39: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02} 39: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02} 39: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02} 39: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01} 39: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02} 39: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02} 39: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02} 39: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02} 39: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02} 39: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01} 39: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01} 39: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01} 39: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01} 39: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01} 39: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01} 39: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01} 39: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01} 39: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01} 39: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01} 39: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01} 39: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01} 39: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01} 39: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01} 39: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01} 39: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01} 39: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01} 39: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01} 39: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01} 39: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01} 39: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01} 39: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01} 39: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01} 39: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02} 39: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01} 39: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01} 39: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01} 39: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01} 39: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01} 39: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01} 39: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01} 39: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01} 39: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02} 39: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02} 39: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02} 39: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02} 39: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01} 39: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01} 39: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01} 39: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01} 39: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01} 39: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01} 39: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01} 39: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01} 39: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01} 39: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01} 39: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01} 39: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01} 39: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01} 39: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01} 39: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01} 39: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02} 39: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01} 39: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01} 39: v (156x3): 39: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 39: Group statistics 39: T-Coupling : 156 (total 156 atoms) 39: Energy Mon. : 156 (total 156 atoms) 39: Acceleration: 156 (total 156 atoms) 39: Freeze : 156 (total 156 atoms) 39: User1 : 156 (total 156 atoms) 39: User2 : 156 (total 156 atoms) 39: VCM : 156 (total 156 atoms) 39: Compressed X: 156 (total 156 atoms) 39: Or. Res. Fit: 156 (total 156 atoms) 39: QMMM : 156 (total 156 atoms) 39: [ OK ] DumpTest.WorksWithTpr (9 ms) 39: [ RUN ] DumpTest.WorksWithTprAndMdpWriting 39: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 39: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 39: [ OK ] DumpTest.WorksWithTprAndMdpWriting (41 ms) 39: [----------] 2 tests from DumpTest (50 ms total) 39: 39: [----------] 4 tests from ReportMethodsTest 39: 39: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 39: For a correct single-point energy evaluation with nsteps = 0, use 39: continuation = yes to avoid constraining the input coordinates. 39: 39: Setting the LD random seed to -208275020 39: Generated 330891 of the 330891 non-bonded parameter combinations 39: Generating 1-4 interactions: fudge = 0.5 39: Generated 330891 of the 330891 1-4 parameter combinations 39: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 39: 39: NOTE 2 [file lysozyme.top, line 1465]: 39: System has non-zero total charge: 2.000000 39: Total charge should normally be an integer. See 39: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 39: for discussion on how close it should be to an integer. 39: 39: 39: 39: Number of degrees of freedom in T-Coupling group rest is 465.00 39: 39: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 39: NVE simulation with an initial temperature of zero: will use a Verlet 39: buffer of 10%. Check your energy drift! 39: 39: 39: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 39: You are using a plain Coulomb cut-off, which might produce artifacts. 39: You might want to consider using PME electrostatics. 39: 39: 39: 39: There were 4 notes 39: Analysing residue names: 39: There are: 10 Protein residues 39: Analysing Protein... 39: This run will generate roughly 0 Mb of data 39: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated 39: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) 39: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted 39: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) 39: [ RUN ] ReportMethodsTest.WritesCorrectInformation 39: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 39: [ OK ] ReportMethodsTest.WritesCorrectInformation (92 ms) 39: [ RUN ] ReportMethodsTest.ToolEndToEndTest 39: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 39: section: Methods 39: subsection: Simulation system 39: A system of 1 molecules (156 atoms) was simulated. 39: 39: subsection: Simulation settings 39: A total of 0 ns were simulated with a time step of 1 fs. 39: Neighbor searching was performed every 10 steps. 39: The Cut-off algorithm was used for electrostatic interactions. 39: with a cut-off of 1 nm. 39: A single cut-off of 1.1 nm was used for Van der Waals interactions. 39: [ OK ] ReportMethodsTest.ToolEndToEndTest (1 ms) 39: [----------] 4 tests from ReportMethodsTest (93 ms total) 39: 39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0 39: Will write tng: Trajectory file (tng format) 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: trr version: GMX_trn_file (single precision) 39: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0 (3 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1 39: Will write tng: Trajectory file (tng format) 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frame 0 time 0.000 39: Precision of /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 39: -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1 (46 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2 39: Will write tng: Trajectory file (tng format) 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2 (3 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3 39: Will write tng: Trajectory file (tng format) 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frames from gro file '', 6 atoms. 39: Reading frame 0 time 0.000 39: Precision of /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 39: -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3 (14 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4 39: Will write tng: Trajectory file (tng format) 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 39: Precision of /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 39: -> frame 0 time 0.000 't= 0.00000', 6 atoms 39: Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4 (3 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5 39: Will write tng: Trajectory file (tng format) 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5 (3 ms) 39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset (72 ms total) 39: 39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0 39: Will write trr: Trajectory in portable xdr format 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0 (1 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1 39: Will write trr: Trajectory in portable xdr format 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frame 0 time 0.000 39: Precision of /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 39: -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1 (1 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2 39: Will write trr: Trajectory in portable xdr format 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2 (1 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3 39: Will write trr: Trajectory in portable xdr format 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frames from gro file '', 6 atoms. 39: Reading frame 0 time 0.000 39: Precision of /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 39: -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3 (1 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4 39: Will write trr: Trajectory in portable xdr format 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 39: Precision of /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 39: -> frame 0 time 0.000 't= 0.00000', 6 atoms 39: Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4 (2 ms) 39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5 39: Will write trr: Trajectory in portable xdr format 39: Group 0 ( System) has 6 elements 39: Group 1 (FirstWaterMolecule) has 3 elements 39: Group 2 (SecondWaterMolecule) has 3 elements 39: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 39: 39: Note that major changes are planned in future for trjconv, to improve usability and utility. 39: Select group for output 39: Selected 2: 'SecondWaterMolecule' 39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5 (1 ms) 39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile (7 ms total) 39: 39: [----------] Global test environment tear-down 39: [==========] 18 tests from 4 test cases ran. (1859 ms total) 39: [ PASSED ] 18 tests. 39/54 Test #39: ToolUnitTests ....................... Passed 1.88 sec test 40 Start 40: FileIOTests 40: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/fileio-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/FileIOTests.xml" 40: Test timeout computed to be: 30 40: [==========] Running 33 tests from 8 test cases. 40: [----------] Global test environment set-up. 40: [----------] 2 tests from FileMD5Test 40: [ RUN ] FileMD5Test.CanComputeMD5 40: [ OK ] FileMD5Test.CanComputeMD5 (113 ms) 40: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 40: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (1 ms) 40: [----------] 2 tests from FileMD5Test (114 ms total) 40: 40: [----------] 3 tests from MrcSerializer 40: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet 40: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) 40: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize 40: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms) 40: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip 40: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (1 ms) 40: [----------] 3 tests from MrcSerializer (1 ms total) 40: 40: [----------] 4 tests from MrcDensityMap 40: [ RUN ] MrcDensityMap.RoundTripIsIdempotent 40: [ OK ] MrcDensityMap.RoundTripIsIdempotent (2 ms) 40: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent 40: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms) 40: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile 40: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms) 40: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile 40: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (11 ms) 40: [----------] 4 tests from MrcDensityMap (13 ms total) 40: 40: [----------] 8 tests from MrcDensityMapHeaderTest 40: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader 40: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) 40: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect 40: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) 40: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid 40: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (1 ms) 40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven 40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) 40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined 40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms) 40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues 40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) 40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents 40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) 40: [ RUN ] MrcDensityMapHeaderTest.IsSane 40: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) 40: [----------] 8 tests from MrcDensityMapHeaderTest (1 ms total) 40: 40: [----------] 9 tests from ReadTest 40: [ RUN ] ReadTest.get_eint_ReadsInteger 40: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 40: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 40: 40: ERROR 1 [file unknown, line 0]: 40: Right hand side '0.8' for parameter 'test' in parameter file is not an 40: integer value 40: 40: 40: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 40: [ RUN ] ReadTest.get_eint_WarnsAboutString 40: 40: ERROR 1 [file unknown, line 0]: 40: Right hand side 'hello' for parameter 'test' in parameter file is not an 40: integer value 40: 40: 40: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 40: [ RUN ] ReadTest.get_eint64_ReadsInteger 40: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 40: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 40: 40: ERROR 1 [file unknown, line 0]: 40: Right hand side '0.8' for parameter 'test' in parameter file is not an 40: integer value 40: 40: 40: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 40: [ RUN ] ReadTest.get_eint64_WarnsAboutString 40: 40: ERROR 1 [file unknown, line 0]: 40: Right hand side 'hello' for parameter 'test' in parameter file is not an 40: integer value 40: 40: 40: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 40: [ RUN ] ReadTest.get_ereal_ReadsInteger 40: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 40: [ RUN ] ReadTest.get_ereal_ReadsFloat 40: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 40: [ RUN ] ReadTest.get_ereal_WarnsAboutString 40: 40: ERROR 1 [file unknown, line 0]: 40: Right hand side 'hello' for parameter 'test' in parameter file is not a 40: real value 40: 40: 40: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 40: [----------] 9 tests from ReadTest (0 ms total) 40: 40: [----------] 1 test from FileIOXdrSerializerTest 40: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect 40: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (0 ms) 40: [----------] 1 test from FileIOXdrSerializerTest (0 ms total) 40: 40: [----------] 2 tests from TngTest 40: [ RUN ] TngTest.CanOpenTngFile 40: TNG library: Cannot open file spc2-traj.tng. ./src/external/tng_io/src/lib/tng_io.c: 890 40: TNG library: Cannot open file spc2-traj.tng. ./src/external/tng_io/src/lib/tng_io.c: 890 40: [ OK ] TngTest.CanOpenTngFile (1 ms) 40: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 40: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 40: [----------] 2 tests from TngTest (1 ms total) 40: 40: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (2 ms) 40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (0 ms) 40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (3 ms) 40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (1 ms) 40: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (6 ms total) 40: 40: [----------] Global test environment tear-down 40: [==========] 33 tests from 8 test cases ran. (136 ms total) 40: [ PASSED ] 33 tests. 40/54 Test #40: FileIOTests ......................... Passed 0.15 sec test 41 Start 41: SelectionUnitTests 41: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/selection-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/SelectionUnitTests.xml" 41: Test timeout computed to be: 30 41: [==========] Running 192 tests from 11 test cases. 41: [----------] Global test environment set-up. 41: [----------] 1 test from IndexGroupTest 41: [ RUN ] IndexGroupTest.RemovesDuplicates 41: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 41: [----------] 1 test from IndexGroupTest (0 ms total) 41: 41: [----------] 15 tests from IndexBlockTest 41: [ RUN ] IndexBlockTest.CreatesUnknownBlock 41: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms) 41: [ RUN ] IndexBlockTest.CreatesAtomBlock 41: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms) 41: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology 41: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms) 41: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology 41: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (1 ms) 41: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology 41: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms) 41: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology 41: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms) 41: [ RUN ] IndexBlockTest.CreatesSingleBlock 41: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) 41: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 41: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) 41: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 41: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) 41: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 41: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 41: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) 41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 41: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 41: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 41: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 41: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 41: [----------] 15 tests from IndexBlockTest (2 ms total) 41: 41: [----------] 11 tests from IndexMapTest 41: [ RUN ] IndexMapTest.InitializesAtomBlock 41: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms) 41: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 41: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms) 41: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 41: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (1 ms) 41: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 41: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) 41: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 41: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms) 41: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 41: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms) 41: [ RUN ] IndexMapTest.InitializesMoleculeBlock 41: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms) 41: [ RUN ] IndexMapTest.MapsSingleBlock 41: [ OK ] IndexMapTest.MapsSingleBlock (1 ms) 41: [ RUN ] IndexMapTest.MapsResidueBlocks 41: [ OK ] IndexMapTest.MapsResidueBlocks (0 ms) 41: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 41: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms) 41: [ RUN ] IndexMapTest.HandlesMultipleRequests 41: [ OK ] IndexMapTest.HandlesMultipleRequests (0 ms) 41: [----------] 11 tests from IndexMapTest (3 ms total) 41: 41: [----------] 3 tests from IndexGroupsAndNamesTest 41: [ RUN ] IndexGroupsAndNamesTest.containsNames 41: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms) 41: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing 41: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms) 41: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect 41: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (1 ms) 41: [----------] 3 tests from IndexGroupsAndNamesTest (1 ms total) 41: 41: [----------] 15 tests from NeighborhoodSearchTest 41: [ RUN ] NeighborhoodSearchTest.SimpleSearch 41: [ OK ] NeighborhoodSearchTest.SimpleSearch (24 ms) 41: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 41: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (27 ms) 41: [ RUN ] NeighborhoodSearchTest.GridSearchBox 41: [ OK ] NeighborhoodSearchTest.GridSearchBox (5 ms) 41: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 41: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (17 ms) 41: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 41: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (6 ms) 41: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 41: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (3 ms) 41: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 41: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (4 ms) 41: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 41: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (30 ms) 41: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 41: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (39 ms) 41: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 41: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) 41: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 41: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 41: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 41: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 41: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 41: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 41: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 41: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (3 ms) 41: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 41: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (1 ms) 41: [----------] 15 tests from NeighborhoodSearchTest (159 ms total) 41: 41: [----------] 12 tests from PositionCalculationTest 41: [ RUN ] PositionCalculationTest.ComputesAtomPositions 41: [ OK ] PositionCalculationTest.ComputesAtomPositions (0 ms) 41: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 41: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (1 ms) 41: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 41: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (0 ms) 41: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 41: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms) 41: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 41: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms) 41: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 41: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms) 41: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 41: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (1 ms) 41: [ RUN ] PositionCalculationTest.ComputesPositionMask 41: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms) 41: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 41: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms) 41: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 41: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms) 41: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 41: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (0 ms) 41: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 41: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (1 ms) 41: [----------] 12 tests from PositionCalculationTest (3 ms total) 41: 41: [----------] 29 tests from SelectionCollectionTest 41: [ RUN ] SelectionCollectionTest.HandlesNoSelections 41: [ OK ] SelectionCollectionTest.HandlesNoSelections (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 41: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 41: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 41: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (1 ms) 41: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 41: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 41: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 41: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 41: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (1 ms) 41: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 41: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 41: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (1 ms) 41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 41: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (1 ms) 41: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 41: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 41: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 41: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 41: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (1 ms) 41: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 41: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (0 ms) 41: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 41: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (0 ms) 41: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 41: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (1 ms) 41: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 41: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (0 ms) 41: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 41: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (0 ms) 41: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 41: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (1 ms) 41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (0 ms) 41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (1 ms) 41: [----------] 29 tests from SelectionCollectionTest (8 ms total) 41: 41: [----------] 14 tests from SelectionCollectionInteractiveTest 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 41: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (0 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 41: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (0 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 41: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (1 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 41: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (0 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 41: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (0 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 41: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (1 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 41: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (0 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 41: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (0 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 41: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (0 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 41: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (0 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 41: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (1 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 41: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (0 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 41: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (0 ms) 41: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 41: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (0 ms) 41: [----------] 14 tests from SelectionCollectionInteractiveTest (4 ms total) 41: 41: [----------] 66 tests from SelectionCollectionDataTest 41: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 41: [ OK ] SelectionCollectionDataTest.HandlesAllNone (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 41: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesResnr 41: [ OK ] SelectionCollectionDataTest.HandlesResnr (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 41: [ OK ] SelectionCollectionDataTest.HandlesResIndex (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 41: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 41: [ OK ] SelectionCollectionDataTest.HandlesAtomname (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 41: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 41: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesChain 41: [ OK ] SelectionCollectionDataTest.HandlesChain (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesMass 41: [ OK ] SelectionCollectionDataTest.HandlesMass (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesCharge 41: [ OK ] SelectionCollectionDataTest.HandlesCharge (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 41: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 41: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 41: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesBeta 41: [ OK ] SelectionCollectionDataTest.HandlesBeta (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesResname 41: [ OK ] SelectionCollectionDataTest.HandlesResname (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 41: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 41: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 41: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 41: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 41: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 41: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 41: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 41: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (158 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 41: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (3 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 41: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (3 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 41: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (47 ms) 41: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 41: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (2 ms) 41: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 41: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 41: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (2 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 41: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 41: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (2 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 41: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 41: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (2 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 41: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 41: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 41: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 41: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 41: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 41: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 41: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 41: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 41: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 41: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 41: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 41: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 41: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 41: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 41: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 41: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 41: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 41: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 41: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 41: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 41: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 41: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 41: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 41: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 41: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 41: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 41: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 41: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 41: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 41: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (1 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 41: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (0 ms) 41: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 41: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (1 ms) 41: [----------] 66 tests from SelectionCollectionDataTest (260 ms total) 41: 41: [----------] 17 tests from SelectionOptionTest 41: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 41: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 41: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 41: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (0 ms) 41: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 41: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (1 ms) 41: [ RUN ] SelectionOptionTest.ChecksEmptySelections 41: [ OK ] SelectionOptionTest.ChecksEmptySelections (0 ms) 41: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 41: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesTooManySelections 41: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 41: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 41: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (1 ms) 41: [ RUN ] SelectionOptionTest.HandlesAdjuster 41: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 41: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 41: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 41: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 41: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 41: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (1 ms) 41: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 41: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms) 41: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 41: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms) 41: [----------] 17 tests from SelectionOptionTest (3 ms total) 41: 41: [----------] 9 tests from SelectionFileOptionTest 41: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 41: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (0 ms) 41: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 41: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (0 ms) 41: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 41: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (1 ms) 41: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 41: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (0 ms) 41: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 41: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (0 ms) 41: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 41: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (1 ms) 41: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 41: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms) 41: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 41: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (0 ms) 41: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 41: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (1 ms) 41: [----------] 9 tests from SelectionFileOptionTest (3 ms total) 41: 41: [----------] Global test environment tear-down 41: [==========] 192 tests from 11 test cases ran. (446 ms total) 41: [ PASSED ] 192 tests. 41/54 Test #41: SelectionUnitTests .................. Passed 0.47 sec test 42 Start 42: MdrunOutputTests 42: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/MdrunOutputTests.xml" 42: Test timeout computed to be: 600 42: [==========] Running 12 tests from 5 test cases. 42: [----------] Global test environment set-up. 42: [----------] 1 test from MdrunTest 42: [ RUN ] MdrunTest.WritesHelp 42: [ OK ] MdrunTest.WritesHelp (2 ms) 42: [----------] 1 test from MdrunTest (2 ms total) 42: 42: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput 42: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 42: Setting the LD random seed to -1209076226 42: Generated 3 of the 3 non-bonded parameter combinations 42: Generating 1-4 interactions: fudge = 0.5 42: Generated 3 of the 3 1-4 parameter combinations 42: Excluding 2 bonded neighbours molecule type 'SOL' 42: Number of degrees of freedom in T-Coupling group rest is 9.00 42: 42: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 42: NVE simulation: will use the initial temperature of 2573.591 K for 42: determining the Verlet buffer size 42: 42: 42: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 42: You are using a plain Coulomb cut-off, which might produce artifacts. 42: You might want to consider using PME electrostatics. 42: 42: 42: 42: There were 2 notes 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 42: Can not increase nstlist because an NVE ensemble is used 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'spc2' 42: 1 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 42: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm 42: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.006 0.003 197.2 42: (ns/day) (hour/ns) 42: Performance: 56.180 0.427 42: Reading frame 0 time 0.000 42: # Atoms 6 42: Reading frame 1 time 0.001 Last frame 1 time 0.001 42: 42: 42: Item #frames Timestep (ps) 42: Step 2 0.001 42: Time 2 0.001 42: Lambda 0 42: Coords 2 0.001 42: Velocities 0 42: Forces 0 42: Box 2 0.001 42: Checking file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc 42: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (102 ms) 42: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 42: Setting the LD random seed to -289974628 42: Generated 3 of the 3 non-bonded parameter combinations 42: Generating 1-4 interactions: fudge = 0.5 42: Generated 3 of the 3 1-4 parameter combinations 42: Excluding 2 bonded neighbours molecule type 'SOL' 42: Number of degrees of freedom in T-Coupling group rest is 9.00 42: 42: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 42: NVE simulation: will use the initial temperature of 2573.591 K for 42: determining the Verlet buffer size 42: 42: 42: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 42: You are using a plain Coulomb cut-off, which might produce artifacts. 42: You might want to consider using PME electrostatics. 42: 42: 42: 42: There were 2 notes 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 42: Can not increase nstlist because an NVE ensemble is used 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'spc2' 42: 1 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 42: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm 42: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.005 0.003 194.6 42: (ns/day) (hour/ns) 42: Performance: 64.706 0.371 42: Reading frame 0 time 0.000 42: # Atoms 6 42: Reading frame 1 time 0.001 Last frame 1 time 0.001 42: 42: 42: Item #frames Timestep (ps) 42: Step 2 0.001 42: Time 2 0.001 42: Lambda 0 42: Coords 2 0.001 42: Velocities 0 42: Forces 0 42: Box 2 0.001 42: Checking file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc 42: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (8 ms) 42: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 42: Setting the LD random seed to -1614831105 42: Generated 3 of the 3 non-bonded parameter combinations 42: Generating 1-4 interactions: fudge = 0.5 42: Generated 3 of the 3 1-4 parameter combinations 42: Excluding 2 bonded neighbours molecule type 'SOL' 42: Number of degrees of freedom in T-Coupling group rest is 9.00 42: 42: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 42: NVE simulation: will use the initial temperature of 2573.591 K for 42: determining the Verlet buffer size 42: 42: 42: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 42: You are using a plain Coulomb cut-off, which might produce artifacts. 42: You might want to consider using PME electrostatics. 42: 42: 42: 42: There were 2 notes 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 42: Can not increase nstlist because an NVE ensemble is used 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'spc2' 42: 1 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 42: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm 42: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.004 0.002 195.8 42: (ns/day) (hour/ns) 42: Performance: 86.478 0.278 42: Reading frame 0 time 0.000 42: # Atoms 3 42: Reading frame 1 time 0.001 Last frame 1 time 0.001 42: 42: 42: Item #frames Timestep (ps) 42: Step 2 0.001 42: Time 2 0.001 42: Lambda 0 42: Coords 2 0.001 42: Velocities 0 42: Forces 0 42: Box 2 0.001 42: Checking file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc 42: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (8 ms) 42: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (118 ms total) 42: 42: [----------] 2 tests from Argon12/OutputFiles 42: [ RUN ] Argon12/OutputFiles.FilesArePresent/0 42: 42: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 42: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 42: that with the Verlet scheme, nstlist has no effect on the accuracy of 42: your simulation. 42: 42: 42: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 42: Setting nstcalcenergy (100) equal to nstenergy (4) 42: 42: Generated 1 of the 1 non-bonded parameter combinations 42: Excluding 1 bonded neighbours molecule type 'Argon' 42: Number of degrees of freedom in T-Coupling group System is 33.00 42: 42: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 42: NVE simulation: will use the initial temperature of 68.810 K for 42: determining the Verlet buffer size 42: 42: 42: There were 3 notes 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 42: Can not increase nstlist because an NVE ensemble is used 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'Argon' 42: 16 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 42: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 42: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.005 0.002 196.7 42: (ns/day) (hour/ns) 42: Performance: 612.994 0.039 42: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (8 ms) 42: [ RUN ] Argon12/OutputFiles.FilesArePresent/1 42: 42: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 42: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 42: that with the Verlet scheme, nstlist has no effect on the accuracy of 42: your simulation. 42: 42: 42: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 42: Setting nstcalcenergy (100) equal to nstenergy (4) 42: 42: Generated 1 of the 1 non-bonded parameter combinations 42: Excluding 1 bonded neighbours molecule type 'Argon' 42: Number of degrees of freedom in T-Coupling group System is 33.00 42: 42: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 42: NVE simulation: will use the initial temperature of 68.810 K for 42: determining the Verlet buffer size 42: 42: 42: There were 3 notes 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 42: Can not increase nstlist because an NVE ensemble is used 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'Argon' 42: 16 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 42: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 42: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.005 0.003 197.9 42: (ns/day) (hour/ns) 42: Performance: 566.491 0.042 42: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (7 ms) 42: [----------] 2 tests from Argon12/OutputFiles (15 ms total) 42: 42: [----------] 3 tests from MdrunCanWrite/Trajectories 42: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 42: Setting the LD random seed to -32575649 42: Generated 8 of the 10 non-bonded parameter combinations 42: Excluding 2 bonded neighbours molecule type 'Methanol' 42: Excluding 2 bonded neighbours molecule type 'SOL' 42: Number of degrees of freedom in T-Coupling group System is 12.00 42: 42: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: 42: You are using a plain Coulomb cut-off, which might produce artifacts. 42: You might want to consider using PME electrostatics. 42: 42: 42: 42: There was 1 note 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 42: Changing nstlist from 10 to 50, rlist from 1.023 to 1.181 42: 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'spc-and-methanol' 42: 6 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.022 0.011 198.2 42: (ns/day) (hour/ns) 42: Performance: 53.493 0.449 42: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (36 ms) 42: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 42: Setting the LD random seed to -470320291 42: Generated 8 of the 10 non-bonded parameter combinations 42: Excluding 2 bonded neighbours molecule type 'Methanol' 42: Excluding 2 bonded neighbours molecule type 'SOL' 42: Number of degrees of freedom in T-Coupling group System is 12.00 42: 42: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: 42: You are using a plain Coulomb cut-off, which might produce artifacts. 42: You might want to consider using PME electrostatics. 42: 42: 42: 42: There was 1 note 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 42: Changing nstlist from 10 to 50, rlist from 1.023 to 1.181 42: 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'spc-and-methanol' 42: 6 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.014 0.007 197.3 42: (ns/day) (hour/ns) 42: Performance: 86.684 0.277 42: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (15 ms) 42: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 42: Setting the LD random seed to -268705797 42: Generated 8 of the 10 non-bonded parameter combinations 42: Excluding 2 bonded neighbours molecule type 'Methanol' 42: Excluding 2 bonded neighbours molecule type 'SOL' 42: Number of degrees of freedom in T-Coupling group System is 12.00 42: 42: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: 42: You are using a plain Coulomb cut-off, which might produce artifacts. 42: You might want to consider using PME electrostatics. 42: 42: 42: 42: There was 1 note 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 42: Changing nstlist from 10 to 50, rlist from 1.023 to 1.181 42: 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'spc-and-methanol' 42: 6 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.012 0.006 197.6 42: (ns/day) (hour/ns) 42: Performance: 101.733 0.236 42: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (14 ms) 42: [----------] 3 tests from MdrunCanWrite/Trajectories (65 ms total) 42: 42: [----------] 3 tests from MdrunCanWrite/NptTrajectories 42: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 42: Setting the LD random seed to -810025751 42: Generated 8 of the 10 non-bonded parameter combinations 42: Excluding 2 bonded neighbours molecule type 'Methanol' 42: Excluding 2 bonded neighbours molecule type 'SOL' 42: Number of degrees of freedom in T-Coupling group System is 12.00 42: 42: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: 42: You are using a plain Coulomb cut-off, which might produce artifacts. 42: You might want to consider using PME electrostatics. 42: 42: 42: 42: There was 1 note 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 42: Changing nstlist from 10 to 50, rlist from 1.023 to 1.181 42: 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'spc-and-methanol' 42: 2 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.007 0.004 196.5 42: (ns/day) (hour/ns) 42: Performance: 72.084 0.333 42: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (12 ms) 42: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 42: Setting the LD random seed to -757139841 42: Generated 8 of the 10 non-bonded parameter combinations 42: Excluding 2 bonded neighbours molecule type 'Methanol' 42: Excluding 2 bonded neighbours molecule type 'SOL' 42: Number of degrees of freedom in T-Coupling group System is 12.00 42: 42: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 42: You are using a plain Coulomb cut-off, which might produce artifacts. 42: You might want to consider using PME electrostatics. 42: 42: 42: 42: There was 1 note 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 42: Changing nstlist from 10 to 50, rlist from 1.023 to 1.181 42: 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'spc-and-methanol' 42: 2 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.007 0.004 193.0 42: (ns/day) (hour/ns) 42: Performance: 71.902 0.334 42: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (60 ms) 42: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 42: Setting the LD random seed to 2011000215 42: Generated 8 of the 10 non-bonded parameter combinations 42: Excluding 2 bonded neighbours molecule type 'Methanol' 42: Excluding 2 bonded neighbours molecule type 'SOL' 42: Number of degrees of freedom in T-Coupling group System is 12.00 42: 42: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: 42: You are using a plain Coulomb cut-off, which might produce artifacts. 42: You might want to consider using PME electrostatics. 42: 42: 42: 42: There was 1 note 42: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 42: log). 42: The current CPU can measure timings more accurately than the code in 42: mdrun-output-test was configured to use. This might affect your simulation 42: speed as accurate timings are needed for load-balancing. 42: Please consider rebuilding mdrun-output-test with the GMX_USE_RDTSCP=ON CMake option. 42: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 42: Changing nstlist from 10 to 50, rlist from 1.023 to 1.181 42: 42: 42: Using 1 MPI thread 42: 42: Non-default thread affinity set, disabling internal thread affinity 42: 42: Using 2 OpenMP threads 42: 42: starting mdrun 'spc-and-methanol' 42: 2 steps, 0.0 ps. 42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 42: Note that mdrun will redetermine rlist based on the actual pair-list setup 42: This run will generate roughly 0 Mb of data 42: 42: Writing final coordinates. 42: 42: Core t (s) Wall t (s) (%) 42: Time: 0.007 0.003 196.4 42: (ns/day) (hour/ns) 42: Performance: 76.512 0.314 42: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (12 ms) 42: [----------] 3 tests from MdrunCanWrite/NptTrajectories (84 ms total) 42: 42: [----------] Global test environment tear-down 42: [==========] 12 tests from 5 test cases ran. (284 ms total) 42: [ PASSED ] 12 tests. 42/54 Test #42: MdrunOutputTests .................... Passed 0.31 sec test 43 Start 43: MdrunModulesTests 43: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/MdrunModulesTests.xml" 43: Test timeout computed to be: 600 43: [==========] Running 10 tests from 3 test cases. 43: [----------] Global test environment set-up. 43: [----------] 4 tests from DensityFittingTest 43: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct 43: Setting the LD random seed to 1597765791 43: Generated 1 of the 1 non-bonded parameter combinations 43: Excluding 1 bonded neighbours molecule type 'Argon' 43: Number of degrees of freedom in T-Coupling group rest is 33.00 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: 43: Steepest Descents: 43: Tolerance (Fmax) = 1.00000e+01 43: Number of steps = 2 43: 43: Energy minimization reached the maximum number of steps before the forces 43: reached the requested precision Fmax < 10. 43: 43: writing lowest energy coordinates. 43: 43: Steepest Descents did not converge to Fmax < 10 in 3 steps. 43: Potential Energy = -3.85654101644806e+03 43: Maximum force = 2.88468568366558e+03 on atom 3 43: Norm of force = 1.07544474716821e+03 43: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as double precision energy file 43: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 This run will generate roughly 0 Mb of data 43: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (98 ms) 43: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy 43: Setting the LD random seed to -21119043 43: Generated 1 of the 1 non-bonded parameter combinations 43: Excluding 1 bonded neighbours molecule type 'Argon' 43: Number of degrees of freedom in T-Coupling group rest is 33.00 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: 43: Steepest Descents: 43: Tolerance (Fmax) = 1.00000e+01 43: Number of steps = 2 43: 43: Energy minimization reached the maximum number of steps before the forces 43: reached the requested precision Fmax < 10. 43: 43: writing lowest energy coordinates. 43: 43: Steepest Descents did not converge to Fmax < 10 in 3 steps. 43: Potential Energy = -2.71386626596691e+04 43: Maximum force = 4.34097106676756e+03 on atom 2 43: Norm of force = 1.25497916295893e+03 43: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as double precision energy file 43: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 This run will generate roughly 0 Mb of data 43: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (7 ms) 43: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch 43: 43: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:836:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. 43: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (6 ms) 43: [ RUN ] DensityFittingTest.CheckpointWorks 43: 43: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 43: Setting nstcalcenergy (100) equal to nstenergy (2) 43: 43: Setting the LD random seed to -12913697 43: Generated 1 of the 1 non-bonded parameter combinations 43: Excluding 1 bonded neighbours molecule type 'Argon' 43: Number of degrees of freedom in T-Coupling group rest is 33.00 43: 43: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 43: NVE simulation: will use the initial temperature of 68.810 K for 43: determining the Verlet buffer size 43: 43: 43: There were 2 notes 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 43: Can not increase nstlist because an NVE ensemble is used 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: starting mdrun 'Argon' 43: 2 steps, 0.0 ps. 43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K 43: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 43: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 43: Note that mdrun will redetermine rlist based on the actual pair-list setup 43: This run will generate roughly 0 Mb of data 43: 43: Writing final coordinates. 43: 43: Core t (s) Wall t (s) (%) 43: Time: 0.008 0.004 196.4 43: (ns/day) (hour/ns) 43: Performance: 62.152 0.386 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 43: 43: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps 43: Can not increase nstlist because an NVE ensemble is used 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: starting mdrun 'Argon' 43: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps). 43: 43: Writing final coordinates. 43: 43: Core t (s) Wall t (s) (%) 43: Time: 0.005 0.003 194.7 43: (ns/day) (hour/ns) 43: Performance: 163.414 0.147 43: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as double precision energy file 43: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (65 ms) 43: [----------] 4 tests from DensityFittingTest (176 ms total) 43: 43: [----------] 4 tests from MimicTest 43: [ RUN ] MimicTest.OneQuantumMol 43: 43: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 43: For a correct single-point energy evaluation with nsteps = 0, use 43: continuation = yes to avoid constraining the input coordinates. 43: 43: Setting the LD random seed to 1425629694 43: Generated 10 of the 10 non-bonded parameter combinations 43: Generating 1-4 interactions: fudge = 0.5 43: Generated 10 of the 10 1-4 parameter combinations 43: Excluding 2 bonded neighbours molecule type 'SOL' 43: Number of degrees of freedom in T-Coupling group rest is 21.00 43: 43: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 43: NVE simulation with an initial temperature of zero: will use a Verlet 43: buffer of 10%. Check your energy drift! 43: 43: 43: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 43: You are using a plain Coulomb cut-off, which might produce artifacts. 43: You might want to consider using PME electrostatics. 43: 43: 43: 43: There were 3 notes 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 43: Can not increase nstlist because an NVE ensemble is used 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/4water.gro' 43: 43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 43: Reading frame 0 time 0.000 Last frame 0 time 0.000 43: 43: NOTE: 17 % of the run time was spent in pair search, 43: you might want to increase nstlist (this has no effect on accuracy) 43: 43: Core t (s) Wall t (s) (%) 43: Time: 0.001 0.001 187.5 43: (ns/day) (hour/ns) 43: Performance: 163.459 0.147 43: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file 43: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 43: [ OK ] MimicTest.OneQuantumMol (11 ms) 43: [ RUN ] MimicTest.AllQuantumMol 43: 43: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 43: For a correct single-point energy evaluation with nsteps = 0, use 43: continuation = yes to avoid constraining the input coordinates. 43: 43: Setting the LD random seed to 952171357 43: Generated 10 of the 10 non-bonded parameter combinations 43: Generating 1-4 interactions: fudge = 0.5 43: Generated 10 of the 10 1-4 parameter combinations 43: Excluding 2 bonded neighbours molecule type 'SOL' 43: Number of degrees of freedom in T-Coupling group rest is 21.00 43: 43: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 43: NVE simulation with an initial temperature of zero: will use a Verlet 43: buffer of 10%. Check your energy drift! 43: 43: 43: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 43: You are using a plain Coulomb cut-off, which might produce artifacts. 43: You might want to consider using PME electrostatics. 43: 43: 43: 43: There were 3 notes 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 43: Can not increase nstlist because an NVE ensemble is used 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/4water.gro' 43: 43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 43: Reading frame 0 time 0.000 Last frame 0 time 0.000 43: 43: NOTE: 15 % of the run time was spent in pair search, 43: you might want to increase nstlist (this has no effect on accuracy) 43: 43: Core t (s) Wall t (s) (%) 43: Time: 0.001 0.000 184.6 43: (ns/day) (hour/ns) 43: Performance: 206.489 0.116 43: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file 43: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 43: [ OK ] MimicTest.AllQuantumMol (10 ms) 43: [ RUN ] MimicTest.TwoQuantumMol 43: 43: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 43: For a correct single-point energy evaluation with nsteps = 0, use 43: continuation = yes to avoid constraining the input coordinates. 43: 43: Setting the LD random seed to -302023235 43: Generated 10 of the 10 non-bonded parameter combinations 43: Generating 1-4 interactions: fudge = 0.5 43: Generated 10 of the 10 1-4 parameter combinations 43: Excluding 2 bonded neighbours molecule type 'SOL' 43: Number of degrees of freedom in T-Coupling group rest is 21.00 43: 43: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 43: NVE simulation with an initial temperature of zero: will use a Verlet 43: buffer of 10%. Check your energy drift! 43: 43: 43: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 43: You are using a plain Coulomb cut-off, which might produce artifacts. 43: You might want to consider using PME electrostatics. 43: 43: 43: 43: There were 3 notes 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 43: Can not increase nstlist because an NVE ensemble is used 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/4water.gro' 43: 43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 43: Reading frame 0 time 0.000 Last frame 0 time 0.000 43: 43: NOTE: 13 % of the run time was spent in pair search, 43: you might want to increase nstlist (this has no effect on accuracy) 43: 43: Core t (s) Wall t (s) (%) 43: Time: 0.001 0.000 185.2 43: (ns/day) (hour/ns) 43: Performance: 210.202 0.114 43: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file 43: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 43: [ OK ] MimicTest.TwoQuantumMol (7 ms) 43: [ RUN ] MimicTest.BondCuts 43: 43: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 43: For a correct single-point energy evaluation with nsteps = 0, use 43: continuation = yes to avoid constraining the input coordinates. 43: 43: Setting the LD random seed to -709005345 43: Generated 2211 of the 2211 non-bonded parameter combinations 43: Generating 1-4 interactions: fudge = 0.5 43: Generated 2211 of the 2211 1-4 parameter combinations 43: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 43: Number of degrees of freedom in T-Coupling group rest is 66.00 43: 43: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 43: NVE simulation: will use the initial temperature of 300.368 K for 43: determining the Verlet buffer size 43: 43: 43: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 43: You are using a plain Coulomb cut-off, which might produce artifacts. 43: You might want to consider using PME electrostatics. 43: 43: 43: 43: There were 3 notes 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 43: Can not increase nstlist because an NVE ensemble is used 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/ala.gro' 43: 43: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 43: Reading frame 0 time 0.000 Last frame 0 time 0.000 43: 43: NOTE: 18 % of the run time was spent in pair search, 43: you might want to increase nstlist (this has no effect on accuracy) 43: 43: Core t (s) Wall t (s) (%) 43: Time: 0.001 0.001 191.9 43: (ns/day) (hour/ns) 43: Performance: 122.139 0.196 43: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file 43: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 43: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm 43: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm 43: Note that mdrun will redetermine rlist based on the actual pair-list setup 43: This run will generate roughly 0 Mb of data 43: [ OK ] MimicTest.BondCuts (65 ms) 43: [----------] 4 tests from MimicTest (93 ms total) 43: 43: [----------] 2 tests from WithIntegrator/ImdTest 43: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0 43: Setting the LD random seed to 1004911549 43: Generated 20503 of the 20503 non-bonded parameter combinations 43: Generating 1-4 interactions: fudge = 1 43: Generated 17396 of the 20503 1-4 parameter combinations 43: Excluding 3 bonded neighbours molecule type 'Glycine' 43: 43: NOTE 1 [file glycine_vacuo.top, line 12]: 43: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an 43: estimated oscillational period of 1.0e-02 ps, which is less than 10 times 43: the time step of 2.0e-03 ps. 43: Maybe you forgot to change the constraints mdp option. 43: 43: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 43: Number of degrees of freedom in T-Coupling group System is 27.00 43: 43: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]: 43: You are using a plain Coulomb cut-off, which might produce artifacts. 43: You might want to consider using PME electrostatics. 43: 43: 43: 43: There were 2 notes 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 43: Changing nstlist from 10 to 50, rlist from 1.026 to 1.34 43: 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: IMD: Enabled. This simulation will accept incoming IMD connections. 43: IMD: Pulling from IMD remote is enabled (-imdpull). 43: IMD: Setting port for connection requests to 0. 43: IMD: Setting up incoming socket. 43: IMD: Listening for IMD connection on port 34719. 43: IMD: -imdwait not set, starting simulation. 43: starting mdrun 'Glycine' 43: 2 steps, 0.0 ps. 43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 43: Set rlist, assuming 4x4 atom pair-list, to 1.026 nm, buffer size 0.026 nm 43: Note that mdrun will redetermine rlist based on the actual pair-list setup 43: This run will generate roughly 0 Mb of data 43: 43: Writing final coordinates. 43: 43: Core t (s) Wall t (s) (%) 43: Time: 0.006 0.003 196.0 43: (ns/day) (hour/ns) 43: Performance: 173.046 0.139 43: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (205 ms) 43: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1 43: 43: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 43: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not 43: apply to steep. 43: 43: Setting the LD random seed to -35787777 43: Generated 20503 of the 20503 non-bonded parameter combinations 43: Generating 1-4 interactions: fudge = 1 43: Generated 17396 of the 20503 1-4 parameter combinations 43: Excluding 3 bonded neighbours molecule type 'Glycine' 43: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 43: Number of degrees of freedom in T-Coupling group System is 27.00 43: 43: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 43: You are using a plain Coulomb cut-off, which might produce artifacts. 43: You might want to consider using PME electrostatics. 43: 43: 43: 43: There were 2 notes 43: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 43: log). 43: The current CPU can measure timings more accurately than the code in 43: mdrun-modules-test was configured to use. This might affect your simulation 43: speed as accurate timings are needed for load-balancing. 43: Please consider rebuilding mdrun-modules-test with the GMX_USE_RDTSCP=ON CMake option. 43: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 43: 43: Using 1 MPI thread 43: 43: Non-default thread affinity set, disabling internal thread affinity 43: 43: Using 2 OpenMP threads 43: 43: IMD: Enabled. This simulation will accept incoming IMD connections. 43: IMD: Pulling from IMD remote is enabled (-imdpull). 43: IMD: Setting port for connection requests to 0. 43: IMD: Setting up incoming socket. 43: IMD: Listening for IMD connection on port 46307. 43: IMD: -imdwait not set, starting simulation. 43: 43: Steepest Descents: 43: Tolerance (Fmax) = 1.00000e+01 43: Number of steps = 2 43: 43: Energy minimization reached the maximum number of steps before the forces 43: reached the requested precision Fmax < 10. 43: 43: writing lowest energy coordinates. 43: 43: Steepest Descents did not converge to Fmax < 10 in 3 steps. 43: Potential Energy = 1.19770464690297e+03 43: Maximum force = 1.77948604657897e+04 on atom 9 43: Norm of force = 7.87328617833981e+03 43: This run will generate roughly 0 Mb of data 43: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (206 ms) 43: [----------] 2 tests from WithIntegrator/ImdTest (411 ms total) 43: 43: [----------] Global test environment tear-down 43: [==========] 10 tests from 3 test cases ran. (681 ms total) 43: [ PASSED ] 10 tests. 43/54 Test #43: MdrunModulesTests ................... Passed 0.70 sec test 44 Start 44: MdrunIOTests 44: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/MdrunIOTests.xml" 44: Test timeout computed to be: 600 44: [==========] Running 51 tests from 9 test cases. 44: [----------] Global test environment set-up. 44: [----------] 3 tests from GromppTest 44: [ RUN ] GromppTest.EmptyMdpFileWorks 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 44: For a correct single-point energy evaluation with nsteps = 0, use 44: continuation = yes to avoid constraining the input coordinates. 44: 44: Setting the LD random seed to -69208975 44: Generated 8 of the 10 non-bonded parameter combinations 44: Excluding 2 bonded neighbours molecule type 'Methanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group rest is 12.00 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 44: NVE simulation: will use the initial temperature of 1046.791 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 44: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: [ OK ] GromppTest.EmptyMdpFileWorks (4 ms) 44: [ RUN ] GromppTest.SimulatedAnnealingWorks 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 44: For a correct single-point energy evaluation with nsteps = 0, use 44: continuation = yes to avoid constraining the input coordinates. 44: 44: Setting the LD random seed to -541139391 44: Generated 8 of the 10 non-bonded parameter combinations 44: Excluding 2 bonded neighbours molecule type 'Methanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Simulated annealing for group rest: Periodic, 4 timepoints 44: Time (ps) Temperature (K) 44: 0.0 298.0 44: 2.0 320.0 44: 4.0 320.0 44: 6.0 298.0 44: Number of degrees of freedom in T-Coupling group rest is 12.00 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 44: NVE simulation: will use the initial temperature of 1046.791 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 44: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: [ OK ] GromppTest.SimulatedAnnealingWorks (4 ms) 44: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 44: For a correct single-point energy evaluation with nsteps = 0, use 44: continuation = yes to avoid constraining the input coordinates. 44: 44: Setting the LD random seed to -4474113 44: Generated 8 of the 10 non-bonded parameter combinations 44: Excluding 2 bonded neighbours molecule type 'Methanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Simulated annealing for group Methanol: Single, 3 timepoints 44: Time (ps) Temperature (K) 44: 0.0 298.0 44: 3.0 280.0 44: 6.0- 270.0 44: Simulated annealing for group SOL: Periodic, 4 timepoints 44: Time (ps) Temperature (K) 44: 0.0 298.0 44: 2.0 320.0 44: 4.0 320.0 44: 6.0 298.0 44: Number of degrees of freedom in T-Coupling group Methanol is 7.20 44: Number of degrees of freedom in T-Coupling group SOL is 4.80 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 44: NVE simulation: will use the initial temperature of 1046.791 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 44: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (3 ms) 44: [----------] 3 tests from GromppTest (11 ms total) 44: 44: [----------] 6 tests from MdrunTerminationTest 44: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault 44: Setting the LD random seed to 1334501887 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There was 1 note 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 2 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.010 0.005 196.1 44: (ns/day) (hour/ns) 44: Performance: 53.232 0.451 44: Reading toplogy and stuff from /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Setting nsteps to 4 44: Writing statusfile with starting step 0 and length 4 steps... 44: time 0.000 and length 0.004 ps 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.003 0.002 190.6 44: (ns/day) (hour/ns) 44: Performance: 161.588 0.149 44: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (95 ms) 44: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 44: Setting the LD random seed to -171966593 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There was 1 note 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 10 to 1, rlist from 1.025 to 1 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 100 steps, 0.1 ps. 44: 44: Step 4: Run time exceeded 0.000 hours, will terminate the run within 2 steps 44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.003 193.7 44: (ns/day) (hour/ns) 44: Performance: 199.498 0.120 44: Reading toplogy and stuff from /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Setting nsteps to 102 44: Writing statusfile with starting step 0 and length 102 steps... 44: time 0.000 and length 0.102 ps 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 102 steps, 0.1 ps (continuing from step 5, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.009 0.004 197.8 44: (ns/day) (hour/ns) 44: Performance: 1891.055 0.013 44: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (18 ms) 44: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend 44: Setting the LD random seed to -889266985 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There was 1 note 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 2 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.004 0.002 196.2 44: (ns/day) (hour/ns) 44: Performance: 116.761 0.206 44: Reading toplogy and stuff from /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Setting nsteps to 4 44: Writing statusfile with starting step 0 and length 4 steps... 44: time 0.000 and length 0.004 ps 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.041 0.021 199.4 44: (ns/day) (hour/ns) 44: Performance: 12.511 1.918 44: Reading toplogy and stuff from /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Setting nsteps to 6 44: Writing statusfile with starting step 0 and length 6 steps... 44: time 0.000 and length 0.006 ps 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.011 0.006 198.6 44: (ns/day) (hour/ns) 44: Performance: 45.725 0.525 44: Reading toplogy and stuff from /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Setting nsteps to 8 44: Writing statusfile with starting step 0 and length 8 steps... 44: time 0.000 and length 0.008 ps 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.007 0.004 197.9 44: (ns/day) (hour/ns) 44: Performance: 72.974 0.329 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: NOTE: 22 % of the run time was spent in pair search, 44: you might want to increase nstlist (this has no effect on accuracy) 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.000 0.000 172.7 44: (ns/day) (hour/ns) 44: Performance: 353.205 0.068 44: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (54 ms) 44: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile 44: Setting the LD random seed to 1827270247 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There was 1 note 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 2 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.003 193.7 44: (ns/day) (hour/ns) 44: Performance: 99.776 0.241 44: Reading toplogy and stuff from /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Setting nsteps to 4 44: Writing statusfile with starting step 0 and length 4 steps... 44: time 0.000 and length 0.004 ps 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 4 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.006 0.003 193.6 44: (ns/day) (hour/ns) 44: Performance: 149.451 0.161 44: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (18 ms) 44: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile 44: Setting the LD random seed to 2093743807 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There was 1 note 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 2 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.369 0.185 199.8 44: (ns/day) (hour/ns) 44: Performance: 1.404 17.098 44: Reading toplogy and stuff from /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Setting nsteps to 4 44: Writing statusfile with starting step 0 and length 4 steps... 44: time 0.000 and length 0.004 ps 44: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (243 ms) 44: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles 44: Setting the LD random seed to -1154371603 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There was 1 note 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 2 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.013 0.007 197.0 44: (ns/day) (hour/ns) 44: Performance: 37.934 0.633 44: Reading toplogy and stuff from /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Setting nsteps to 4 44: Writing statusfile with starting step 0 and length 4 steps... 44: time 0.000 and length 0.004 ps 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.006 0.003 197.6 44: (ns/day) (hour/ns) 44: Performance: 86.297 0.278 44: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (25 ms) 44: [----------] 6 tests from MdrunTerminationTest (453 ms total) 44: 44: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.011 0.006 196.3 44: (ns/day) (hour/ns) 44: Performance: 265.680 0.090 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.088 0.044 199.6 44: (ns/day) (hour/ns) 44: Performance: 17.664 1.359 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.010 0.005 197.8 44: (ns/day) (hour/ns) 44: Performance: 158.003 0.152 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (77 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.012 0.006 198.1 44: (ns/day) (hour/ns) 44: Performance: 236.727 0.101 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.239 0.120 199.9 44: (ns/day) (hour/ns) 44: Performance: 6.496 3.694 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.006 0.003 198.4 44: (ns/day) (hour/ns) 44: Performance: 239.710 0.100 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (153 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.003 196.5 44: (ns/day) (hour/ns) 44: Performance: 568.425 0.042 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.003 194.2 44: (ns/day) (hour/ns) 44: Performance: 300.848 0.080 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.006 0.003 197.6 44: (ns/day) (hour/ns) 44: Performance: 259.404 0.093 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (23 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.010 0.005 197.2 44: (ns/day) (hour/ns) 44: Performance: 283.637 0.085 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.030 0.015 198.7 44: (ns/day) (hour/ns) 44: Performance: 51.953 0.462 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.009 0.004 195.3 44: (ns/day) (hour/ns) 44: Performance: 173.484 0.138 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (52 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: NVE simulation: will use the initial temperature of 2573.591 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 4 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: NVE simulation: will use the initial temperature of 2573.591 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 4 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.007 0.004 196.4 44: (ns/day) (hour/ns) 44: Performance: 417.384 0.058 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.003 196.9 44: (ns/day) (hour/ns) 44: Performance: 307.630 0.078 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.003 195.1 44: (ns/day) (hour/ns) 44: Performance: 305.870 0.078 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (27 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: NVE simulation: will use the initial temperature of 2573.591 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 4 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: NVE simulation: will use the initial temperature of 2573.591 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 4 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.015 0.007 198.7 44: (ns/day) (hour/ns) 44: Performance: 198.275 0.121 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.007 0.003 198.1 44: (ns/day) (hour/ns) 44: Performance: 228.684 0.105 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.007 0.003 198.2 44: (ns/day) (hour/ns) 44: Performance: 223.865 0.107 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (84 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.007 0.004 196.7 44: (ns/day) (hour/ns) 44: Performance: 416.538 0.058 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.002 194.0 44: (ns/day) (hour/ns) 44: Performance: 333.213 0.072 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.003 194.3 44: (ns/day) (hour/ns) 44: Performance: 285.395 0.084 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (73 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 3 of the 3 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 3 of the 3 1-4 parameter combinations 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 9.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 25, rlist from 0.754 to 0.9 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.010 0.005 195.2 44: (ns/day) (hour/ns) 44: Performance: 285.305 0.084 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 25, rlist from 0.754 to 0.9 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.008 0.004 194.1 44: (ns/day) (hour/ns) 44: Performance: 197.487 0.122 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 25, rlist from 0.754 to 0.9 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc2' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.008 0.004 194.8 44: (ns/day) (hour/ns) 44: Performance: 179.905 0.133 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (38 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2145 of the 2145 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2145 of the 2145 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 44: 44: NOTE 3 [file unknown]: 44: You are using constraints on all bonds, whereas the forcefield has been 44: parametrized only with constraints involving hydrogen atoms. We suggest 44: using constraints = h-bonds instead, this will also improve performance. 44: 44: Cleaning up constraints and constant bonded interactions with virtual sites 44: Removed 18 Angles with virtual sites, 21 left 44: Removed 10 Proper Dih.s with virtual sites, 44 left 44: Converted 15 Constraints with virtual sites to connections, 7 left 44: Number of degrees of freedom in T-Coupling group System is 23.00 44: 44: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: NVE simulation: will use the initial temperature of 456.887 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 5 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: There are 9 non-linear virtual site constructions. Their contribution to 44: the energy error is approximated. In most cases this does not affect the 44: error significantly. 44: 44: 44: NOTE 6 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 6 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2145 of the 2145 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2145 of the 2145 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 44: 44: NOTE 3 [file unknown]: 44: You are using constraints on all bonds, whereas the forcefield has been 44: parametrized only with constraints involving hydrogen atoms. We suggest 44: using constraints = h-bonds instead, this will also improve performance. 44: 44: Cleaning up constraints and constant bonded interactions with virtual sites 44: Removed 18 Angles with virtual sites, 21 left 44: Removed 10 Proper Dih.s with virtual sites, 44 left 44: Converted 15 Constraints with virtual sites to connections, 7 left 44: Number of degrees of freedom in T-Coupling group System is 23.00 44: 44: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: NVE simulation: will use the initial temperature of 456.887 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 5 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: There are 9 non-linear virtual site constructions. Their contribution to 44: the energy error is approximated. In most cases this does not affect the 44: error significantly. 44: 44: 44: NOTE 6 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 6 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 16 steps, 0.0 ps. 44: turning all bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: turning all bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.014 0.007 196.6 44: (ns/day) (hour/ns) 44: Performance: 199.682 0.120 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.010 0.005 194.7 44: (ns/day) (hour/ns) 44: Performance: 148.028 0.162 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.097 0.049 199.4 44: (ns/day) (hour/ns) 44: Performance: 16.010 1.499 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (161 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2145 of the 2145 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2145 of the 2145 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 44: 44: NOTE 3 [file unknown]: 44: You are using constraints on all bonds, whereas the forcefield has been 44: parametrized only with constraints involving hydrogen atoms. We suggest 44: using constraints = h-bonds instead, this will also improve performance. 44: 44: Cleaning up constraints and constant bonded interactions with virtual sites 44: Removed 18 Angles with virtual sites, 21 left 44: Removed 10 Proper Dih.s with virtual sites, 44 left 44: Converted 15 Constraints with virtual sites to connections, 7 left 44: Number of degrees of freedom in T-Coupling group System is 23.00 44: 44: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: NVE simulation: will use the initial temperature of 456.887 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 5 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: There are 9 non-linear virtual site constructions. Their contribution to 44: the energy error is approximated. In most cases this does not affect the 44: error significantly. 44: 44: 44: NOTE 6 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 6 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2145 of the 2145 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2145 of the 2145 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 44: 44: NOTE 3 [file unknown]: 44: You are using constraints on all bonds, whereas the forcefield has been 44: parametrized only with constraints involving hydrogen atoms. We suggest 44: using constraints = h-bonds instead, this will also improve performance. 44: 44: Cleaning up constraints and constant bonded interactions with virtual sites 44: Removed 18 Angles with virtual sites, 21 left 44: Removed 10 Proper Dih.s with virtual sites, 44 left 44: Converted 15 Constraints with virtual sites to connections, 7 left 44: Number of degrees of freedom in T-Coupling group System is 23.00 44: 44: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: NVE simulation: will use the initial temperature of 456.887 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 5 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: There are 9 non-linear virtual site constructions. Their contribution to 44: the energy error is approximated. In most cases this does not affect the 44: error significantly. 44: 44: 44: NOTE 6 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 6 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 16 steps, 0.0 ps. 44: turning all bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: turning all bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.073 0.037 199.1 44: (ns/day) (hour/ns) 44: Performance: 39.985 0.600 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.013 0.007 196.8 44: (ns/day) (hour/ns) 44: Performance: 114.354 0.210 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.010 0.005 193.9 44: (ns/day) (hour/ns) 44: Performance: 157.758 0.152 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (135 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2145 of the 2145 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2145 of the 2145 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 44: 44: NOTE 3 [file unknown]: 44: You are using constraints on all bonds, whereas the forcefield has been 44: parametrized only with constraints involving hydrogen atoms. We suggest 44: using constraints = h-bonds instead, this will also improve performance. 44: 44: Cleaning up constraints and constant bonded interactions with virtual sites 44: Removed 18 Angles with virtual sites, 21 left 44: Removed 10 Proper Dih.s with virtual sites, 44 left 44: Converted 15 Constraints with virtual sites to connections, 7 left 44: Number of degrees of freedom in T-Coupling group System is 23.00 44: 44: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 44: There are 9 non-linear virtual site constructions. Their contribution to 44: the energy error is approximated. In most cases this does not affect the 44: error significantly. 44: 44: 44: NOTE 5 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 5 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2145 of the 2145 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2145 of the 2145 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 44: 44: NOTE 3 [file unknown]: 44: You are using constraints on all bonds, whereas the forcefield has been 44: parametrized only with constraints involving hydrogen atoms. We suggest 44: using constraints = h-bonds instead, this will also improve performance. 44: 44: Cleaning up constraints and constant bonded interactions with virtual sites 44: Removed 18 Angles with virtual sites, 21 left 44: Removed 10 Proper Dih.s with virtual sites, 44 left 44: Converted 15 Constraints with virtual sites to connections, 7 left 44: Number of degrees of freedom in T-Coupling group System is 23.00 44: 44: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 44: There are 9 non-linear virtual site constructions. Their contribution to 44: the energy error is approximated. In most cases this does not affect the 44: error significantly. 44: 44: 44: NOTE 5 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 5 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.745 to 0.873 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 16 steps, 0.0 ps. 44: turning all bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: turning all bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.019 0.009 197.8 44: (ns/day) (hour/ns) 44: Performance: 156.424 0.153 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.745 to 0.873 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.010 0.005 194.8 44: (ns/day) (hour/ns) 44: Performance: 145.466 0.165 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.745 to 0.873 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.012 0.006 196.0 44: (ns/day) (hour/ns) 44: Performance: 130.863 0.183 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (213 ms) 44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2145 of the 2145 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2145 of the 2145 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 44: 44: NOTE 3 [file unknown]: 44: You are using constraints on all bonds, whereas the forcefield has been 44: parametrized only with constraints involving hydrogen atoms. We suggest 44: using constraints = h-bonds instead, this will also improve performance. 44: 44: Cleaning up constraints and constant bonded interactions with virtual sites 44: Removed 18 Angles with virtual sites, 21 left 44: Removed 10 Proper Dih.s with virtual sites, 44 left 44: Converted 15 Constraints with virtual sites to connections, 7 left 44: Number of degrees of freedom in T-Coupling group System is 23.00 44: 44: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 44: There are 9 non-linear virtual site constructions. Their contribution to 44: the energy error is approximated. In most cases this does not affect the 44: error significantly. 44: 44: 44: NOTE 5 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 5 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2145 of the 2145 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2145 of the 2145 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 44: 44: NOTE 3 [file unknown]: 44: You are using constraints on all bonds, whereas the forcefield has been 44: parametrized only with constraints involving hydrogen atoms. We suggest 44: using constraints = h-bonds instead, this will also improve performance. 44: 44: Cleaning up constraints and constant bonded interactions with virtual sites 44: Removed 18 Angles with virtual sites, 21 left 44: Removed 10 Proper Dih.s with virtual sites, 44 left 44: Converted 15 Constraints with virtual sites to connections, 7 left 44: Number of degrees of freedom in T-Coupling group System is 23.00 44: 44: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 44: There are 9 non-linear virtual site constructions. Their contribution to 44: the energy error is approximated. In most cases this does not affect the 44: error significantly. 44: 44: 44: NOTE 5 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 5 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 40, rlist from 0.727 to 0.874 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 16 steps, 0.0 ps. 44: turning all bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: turning all bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.014 0.007 197.6 44: (ns/day) (hour/ns) 44: Performance: 206.697 0.116 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 40, rlist from 0.727 to 0.874 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.012 0.006 197.3 44: (ns/day) (hour/ns) 44: Performance: 124.699 0.192 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 40, rlist from 0.727 to 0.874 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Alanine dipeptide in vacuo' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.013 0.006 197.7 44: (ns/day) (hour/ns) 44: Performance: 122.585 0.196 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (184 ms) 44: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (1221 ms total) 44: 44: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact 44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2485 of the 2485 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2485 of the 2485 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'nonanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 79.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: NVE simulation: will use the initial temperature of 293.480 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 4 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2485 of the 2485 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2485 of the 2485 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'nonanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 79.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: NVE simulation: will use the initial temperature of 293.480 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 4 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 16 steps, 0.0 ps. 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.010 0.005 196.6 44: (ns/day) (hour/ns) 44: Performance: 289.556 0.083 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.011 0.006 195.3 44: (ns/day) (hour/ns) 44: Performance: 140.958 0.170 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.008 0.004 195.3 44: (ns/day) (hour/ns) 44: Performance: 200.214 0.120 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (115 ms) 44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2485 of the 2485 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2485 of the 2485 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'nonanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 79.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: NVE simulation: will use the initial temperature of 293.480 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 4 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2485 of the 2485 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2485 of the 2485 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'nonanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 79.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: NVE simulation: will use the initial temperature of 293.480 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 4 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 16 steps, 0.0 ps. 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.011 0.006 198.8 44: (ns/day) (hour/ns) 44: Performance: 266.312 0.090 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.010 0.005 198.4 44: (ns/day) (hour/ns) 44: Performance: 149.213 0.161 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.009 0.004 198.3 44: (ns/day) (hour/ns) 44: Performance: 180.502 0.133 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (102 ms) 44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2485 of the 2485 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2485 of the 2485 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'nonanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 79.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2485 of the 2485 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2485 of the 2485 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'nonanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 79.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.728 to 0.807 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 16 steps, 0.0 ps. 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.013 0.007 196.2 44: (ns/day) (hour/ns) 44: Performance: 224.888 0.107 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.728 to 0.807 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: NOTE: 32 % of the run time was spent in pair search, 44: you might want to increase nstlist (this has no effect on accuracy) 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.020 0.010 195.5 44: (ns/day) (hour/ns) 44: Performance: 74.707 0.321 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.728 to 0.807 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.102 0.051 199.4 44: (ns/day) (hour/ns) 44: Performance: 15.201 1.579 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (248 ms) 44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2485 of the 2485 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2485 of the 2485 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'nonanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 79.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 2485 of the 2485 non-bonded parameter combinations 44: Generating 1-4 interactions: fudge = 0.5 44: Generated 2485 of the 2485 1-4 parameter combinations 44: Excluding 3 bonded neighbours molecule type 'nonanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group System is 79.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 16 steps, 0.0 ps. 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.014 0.007 197.4 44: (ns/day) (hour/ns) 44: Performance: 201.947 0.119 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.013 0.007 192.9 44: (ns/day) (hour/ns) 44: Performance: 118.059 0.203 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun '30 system in water' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.013 0.007 195.7 44: (ns/day) (hour/ns) 44: Performance: 117.210 0.205 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (142 ms) 44: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (607 ms total) 44: 44: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact 44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.007 0.003 196.4 44: (ns/day) (hour/ns) 44: Performance: 431.959 0.056 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.099 0.050 199.7 44: (ns/day) (hour/ns) 44: Performance: 15.671 1.531 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.006 0.003 194.6 44: (ns/day) (hour/ns) 44: Performance: 256.004 0.094 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (71 ms) 44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.008 0.004 196.3 44: (ns/day) (hour/ns) 44: Performance: 348.746 0.069 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.006 0.003 197.0 44: (ns/day) (hour/ns) 44: Performance: 275.697 0.087 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.003 194.8 44: (ns/day) (hour/ns) 44: Performance: 276.023 0.087 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (24 ms) 44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.109 0.055 199.7 44: (ns/day) (hour/ns) 44: Performance: 26.893 0.892 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.010 0.005 197.1 44: (ns/day) (hour/ns) 44: Performance: 159.486 0.150 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.007 0.004 195.5 44: (ns/day) (hour/ns) 44: Performance: 208.735 0.115 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (80 ms) 44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.007 0.004 197.7 44: (ns/day) (hour/ns) 44: Performance: 401.944 0.060 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.008 0.004 196.5 44: (ns/day) (hour/ns) 44: Performance: 180.792 0.133 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.003 195.7 44: (ns/day) (hour/ns) 44: Performance: 284.697 0.084 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (25 ms) 44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.011 0.006 198.1 44: (ns/day) (hour/ns) 44: Performance: 262.320 0.091 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.011 0.005 198.0 44: (ns/day) (hour/ns) 44: Performance: 145.739 0.165 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.007 0.003 198.4 44: (ns/day) (hour/ns) 44: Performance: 222.218 0.108 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (81 ms) 44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.008 0.004 196.9 44: (ns/day) (hour/ns) 44: Performance: 376.818 0.064 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.013 0.007 197.5 44: (ns/day) (hour/ns) 44: Performance: 119.534 0.201 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.118 0.059 199.7 44: (ns/day) (hour/ns) 44: Performance: 13.130 1.828 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (87 ms) 44: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact (368 ms total) 44: 44: [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact 44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.009 0.004 196.1 44: (ns/day) (hour/ns) 44: Performance: 327.169 0.073 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.007 0.003 195.3 44: (ns/day) (hour/ns) 44: Performance: 231.180 0.104 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.006 0.003 195.5 44: (ns/day) (hour/ns) 44: Performance: 274.305 0.087 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (30 ms) 44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.006 0.003 196.8 44: (ns/day) (hour/ns) 44: Performance: 510.659 0.047 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.011 0.005 197.3 44: (ns/day) (hour/ns) 44: Performance: 143.173 0.168 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.007 0.004 195.9 44: (ns/day) (hour/ns) 44: Performance: 212.074 0.113 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (73 ms) 44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.008 0.004 196.5 44: (ns/day) (hour/ns) 44: Performance: 340.101 0.071 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.006 0.003 190.2 44: (ns/day) (hour/ns) 44: Performance: 240.275 0.100 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.006 0.003 194.9 44: (ns/day) (hour/ns) 44: Performance: 245.133 0.098 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (30 ms) 44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: NVE simulation: will use the initial temperature of 68.810 K for 44: determining the Verlet buffer size 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.013 0.007 198.1 44: (ns/day) (hour/ns) 44: Performance: 216.938 0.111 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.008 0.004 197.6 44: (ns/day) (hour/ns) 44: Performance: 186.541 0.129 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.008 0.004 198.1 44: (ns/day) (hour/ns) 44: Performance: 195.451 0.123 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (84 ms) 44: [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact (218 ms total) 44: 44: [----------] 12 tests from NPT/MdrunNoAppendContinuationIsExact 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.006 0.003 195.0 44: (ns/day) (hour/ns) 44: Performance: 452.719 0.053 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.008 0.004 195.6 44: (ns/day) (hour/ns) 44: Performance: 188.886 0.127 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.008 0.004 196.1 44: (ns/day) (hour/ns) 44: Performance: 198.219 0.121 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (78 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.008 0.004 193.8 44: (ns/day) (hour/ns) 44: Performance: 374.800 0.064 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.008 0.004 194.2 44: (ns/day) (hour/ns) 44: Performance: 187.658 0.128 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.008 0.004 194.8 44: (ns/day) (hour/ns) 44: Performance: 185.007 0.130 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (30 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.099 0.049 199.5 44: (ns/day) (hour/ns) 44: Performance: 29.690 0.808 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.011 0.006 196.4 44: (ns/day) (hour/ns) 44: Performance: 141.355 0.170 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.007 0.003 195.1 44: (ns/day) (hour/ns) 44: Performance: 228.989 0.105 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (82 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.008 0.004 194.4 44: (ns/day) (hour/ns) 44: Performance: 379.324 0.063 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.008 0.004 195.4 44: (ns/day) (hour/ns) 44: Performance: 194.635 0.123 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.007 0.004 197.0 44: (ns/day) (hour/ns) 44: Performance: 207.224 0.116 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (27 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 44: 44: 44: WARNING 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: Using Berendsen pressure coupling invalidates the true ensemble for the 44: thermostat 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: 44: There was 1 warning 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 44: 44: 44: WARNING 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 44: Using Berendsen pressure coupling invalidates the true ensemble for the 44: thermostat 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: 44: There was 1 warning 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.014 0.007 197.8 44: (ns/day) (hour/ns) 44: Performance: 201.702 0.119 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.018 0.009 198.1 44: (ns/day) (hour/ns) 44: Performance: 83.423 0.288 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.008 0.004 195.8 44: (ns/day) (hour/ns) 44: Performance: 188.842 0.127 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (83 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.013 0.007 197.9 44: (ns/day) (hour/ns) 44: Performance: 219.457 0.109 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.007 0.003 196.4 44: (ns/day) (hour/ns) 44: Performance: 230.331 0.104 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.086 0.043 199.6 44: (ns/day) (hour/ns) 44: Performance: 17.974 1.335 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (72 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 44: The Berendsen thermostat does not generate the correct kinetic energy 44: distribution. You might want to consider using the V-rescale thermostat. 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.009 0.005 195.2 44: (ns/day) (hour/ns) 44: Performance: 312.768 0.077 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.007 0.004 195.1 44: (ns/day) (hour/ns) 44: Performance: 203.221 0.118 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.008 0.004 194.2 44: (ns/day) (hour/ns) 44: Performance: 196.440 0.122 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (39 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 44: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (0 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.008 0.004 197.4 44: (ns/day) (hour/ns) 44: Performance: 350.631 0.068 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.002 196.0 44: (ns/day) (hour/ns) 44: Performance: 324.462 0.074 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.011 0.006 195.8 44: (ns/day) (hour/ns) 44: Performance: 137.107 0.175 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (68 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.015 0.008 198.9 44: (ns/day) (hour/ns) 44: Performance: 193.638 0.124 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.007 0.004 198.4 44: (ns/day) (hour/ns) 44: Performance: 212.905 0.113 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.008 0.004 198.6 44: (ns/day) (hour/ns) 44: Performance: 196.133 0.122 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (39 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10 44: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (0 ms) 44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11 44: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (0 ms) 44: [----------] 12 tests from NPT/MdrunNoAppendContinuationIsExact (519 ms total) 44: 44: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact 44: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 44: that with the Verlet scheme, nstlist has no effect on the accuracy of 44: your simulation. 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 44: Setting nstcalcenergy (100) equal to nstenergy (4) 44: 44: Generated 1 of the 1 non-bonded parameter combinations 44: Excluding 1 bonded neighbours molecule type 'Argon' 44: Number of degrees of freedom in T-Coupling group System is 33.00 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps. 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.010 0.005 197.0 44: (ns/day) (hour/ns) 44: Performance: 279.038 0.086 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 8 steps, 0.0 ps. 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.008 0.004 195.8 44: (ns/day) (hour/ns) 44: Performance: 181.325 0.132 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 44: 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'Argon' 44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.011 0.005 195.9 44: (ns/day) (hour/ns) 44: Performance: 143.589 0.167 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (79 ms) 44: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (79 ms total) 44: 44: [----------] 3 tests from Checking/InitialConstraintsTest 44: [ RUN ] Checking/InitialConstraintsTest.Works/0 44: Setting the LD random seed to -319308465 44: Generated 8 of the 10 non-bonded parameter combinations 44: Excluding 2 bonded neighbours molecule type 'Methanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group rest is 11.00 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 44: NVE simulation: will use the initial temperature of 1141.954 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc-and-methanol' 44: 1 steps, 0.0 ps. 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 44: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.005 0.003 192.8 44: (ns/day) (hour/ns) 44: Performance: 66.075 0.363 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (15 ms) 44: [ RUN ] Checking/InitialConstraintsTest.Works/1 44: Setting the LD random seed to -134234881 44: Generated 8 of the 10 non-bonded parameter combinations 44: Excluding 2 bonded neighbours molecule type 'Methanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group rest is 11.00 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 44: NVE simulation: will use the initial temperature of 1141.954 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 2 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc-and-methanol' 44: 1 steps, 0.0 ps. 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 44: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.004 0.002 196.9 44: (ns/day) (hour/ns) 44: Performance: 76.148 0.315 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (12 ms) 44: [ RUN ] Checking/InitialConstraintsTest.Works/2 44: 44: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 44: Integrator method md-vv-avek is implemented primarily for validation 44: purposes; for molecular dynamics, you should probably be using md or md-vv 44: 44: Setting the LD random seed to -612377105 44: Generated 8 of the 10 non-bonded parameter combinations 44: Excluding 2 bonded neighbours molecule type 'Methanol' 44: Excluding 2 bonded neighbours molecule type 'SOL' 44: Number of degrees of freedom in T-Coupling group rest is 11.00 44: 44: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 44: NVE simulation: will use the initial temperature of 1141.954 K for 44: determining the Verlet buffer size 44: 44: 44: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 44: You are using a plain Coulomb cut-off, which might produce artifacts. 44: You might want to consider using PME electrostatics. 44: 44: 44: 44: There were 3 notes 44: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 44: log). 44: The current CPU can measure timings more accurately than the code in 44: mdrun-io-test was configured to use. This might affect your simulation 44: speed as accurate timings are needed for load-balancing. 44: Please consider rebuilding mdrun-io-test with the GMX_USE_RDTSCP=ON CMake option. 44: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 44: Can not increase nstlist because an NVE ensemble is used 44: 44: Using 1 MPI thread 44: 44: Non-default thread affinity set, disabling internal thread affinity 44: 44: Using 2 OpenMP threads 44: 44: starting mdrun 'spc-and-methanol' 44: 1 steps, 0.0 ps. 44: turning H bonds into constraints... 44: turning H bonds into constraints... 44: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 44: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm 44: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm 44: Note that mdrun will redetermine rlist based on the actual pair-list setup 44: This run will generate roughly 0 Mb of data 44: 44: Writing final coordinates. 44: 44: Core t (s) Wall t (s) (%) 44: Time: 0.004 0.002 191.6 44: (ns/day) (hour/ns) 44: Performance: 75.742 0.317 44: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as double precision energy file 44: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (53 ms) 44: [----------] 3 tests from Checking/InitialConstraintsTest (80 ms total) 44: 44: [----------] Global test environment tear-down 44: [==========] 51 tests from 9 test cases ran. (3557 ms total) 44: [ PASSED ] 51 tests. 44/54 Test #44: MdrunIOTests ........................ Passed 3.59 sec test 45 Start 45: MdrunTests 45: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/mdrun-test "-ntomp" "2" "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/MdrunTests.xml" 45: Test timeout computed to be: 600 45: [==========] Running 24 tests from 7 test cases. 45: [----------] Global test environment set-up. 45: [----------] 1 test from DispersionCorrectionTest 45: [ RUN ] DispersionCorrectionTest.DispersionCorrectionCanRun 45: 45: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 45: The Berendsen thermostat does not generate the correct kinetic energy 45: distribution. You might want to consider using the V-rescale thermostat. 45: 45: Setting the LD random seed to 2146433023 45: Generated 2145 of the 2145 non-bonded parameter combinations 45: Generating 1-4 interactions: fudge = 0.5 45: Generated 2145 of the 2145 1-4 parameter combinations 45: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 45: Cleaning up constraints and constant bonded interactions with virtual sites 45: Converted 3 Bonds with virtual sites to connections, 7 left 45: Removed 18 Angles with virtual sites, 21 left 45: Removed 10 Proper Dih.s with virtual sites, 44 left 45: Converted 12 Constraints with virtual sites to connections, 0 left 45: Number of degrees of freedom in T-Coupling group System is 30.00 45: 45: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 45: There are 9 non-linear virtual site constructions. Their contribution to 45: the energy error is approximated. In most cases this does not affect the 45: error significantly. 45: 45: 45: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 45: You are using a plain Coulomb cut-off, which might produce artifacts. 45: You might want to consider using PME electrostatics. 45: 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Changing nstlist from 10 to 40, rlist from 1.019 to 1.138 45: 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'Alanine dipeptide in vacuo' 45: 200 steps, 0.4 ps. 45: turning H bonds into constraints... 45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 45: Calculated rlist for 1x1 atom pair-list as 1.028 nm, buffer size 0.028 nm 45: Set rlist, assuming 4x4 atom pair-list, to 1.016 nm, buffer size 0.016 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: This run will generate roughly 0 Mb of data 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.053 0.026 199.2 45: (ns/day) (hour/ns) 45: Performance: 1313.757 0.018 45: [ OK ] DispersionCorrectionTest.DispersionCorrectionCanRun (160 ms) 45: [----------] 1 test from DispersionCorrectionTest (160 ms total) 45: 45: [----------] 1 test from OriresTest 45: [ RUN ] OriresTest.OriresCanRun 45: 45: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: 45: The Berendsen thermostat does not generate the correct kinetic energy 45: distribution. You might want to consider using the V-rescale thermostat. 45: 45: Setting the LD random seed to 872411903 45: Generated 2145 of the 2145 non-bonded parameter combinations 45: Generating 1-4 interactions: fudge = 0.5 45: Generated 2145 of the 2145 1-4 parameter combinations 45: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 45: Excluding 2 bonded neighbours molecule type 'SOL' 45: Number of degrees of freedom in T-Coupling group System is 518.00 45: 45: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: 45: You are using a plain Coulomb cut-off, which might produce artifacts. 45: You might want to consider using PME electrostatics. 45: 45: 45: 45: There were 2 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: 45: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank. 45: Changing nstlist from 10 to 25, rlist from 1.059 to 1.178 45: 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1' 45: 10 steps, 0.0 ps. 45: turning H bonds into constraints... 45: turning H bonds into constraints... 45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 45: Calculated rlist for 1x1 atom pair-list as 1.073 nm, buffer size 0.073 nm 45: Set rlist, assuming 4x4 atom pair-list, to 1.054 nm, buffer size 0.054 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: This run will generate roughly 0 Mb of data 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.022 0.011 198.0 45: (ns/day) (hour/ns) 45: Performance: 173.682 0.138 45: [ OK ] OriresTest.OriresCanRun (512 ms) 45: [----------] 1 test from OriresTest (512 ms total) 45: 45: [----------] 3 tests from PmeTest 45: [ RUN ] PmeTest.ReproducesEnergies 45: Setting the LD random seed to 2113634255 45: Generated 8 of the 10 non-bonded parameter combinations 45: Excluding 2 bonded neighbours molecule type 'Methanol' 45: Excluding 2 bonded neighbours molecule type 'SOL' 45: Number of degrees of freedom in T-Coupling group rest is 12.00 45: 45: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]: 45: NVE simulation: will use the initial temperature of 1046.791 K for 45: determining the Verlet buffer size 45: 45: Estimate for the relative computational load of the PME mesh part: 1.00 45: 45: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]: 45: The optimal PME mesh load for parallel simulations is below 0.5 45: and for highly parallel simulations between 0.25 and 0.33, 45: for higher performance, increase the cut-off and the PME grid spacing. 45: 45: 45: 45: There were 2 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc-and-methanol' 45: 20 steps, 0.0 ps. 45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 45: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 45: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: Calculating fourier grid dimensions for X Y Z 45: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 45: This run will generate roughly 0 Mb of data 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.044 0.022 198.9 45: (ns/day) (hour/ns) 45: Performance: 82.227 0.292 45: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as double precision energy file 45: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc-and-methanol' 45: 20 steps, 0.0 ps. 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.040 0.020 198.9 45: (ns/day) (hour/ns) 45: Performance: 89.674 0.268 45: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as double precision energy file 45: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc-and-methanol' 45: 20 steps, 0.0 ps. 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.049 0.025 199.3 45: (ns/day) (hour/ns) 45: Performance: 73.453 0.327 45: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as double precision energy file 45: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (416 ms) 45: [ RUN ] PmeTest.ScalesTheBox 45: 45: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 45: For a correct single-point energy evaluation with nsteps = 0, use 45: continuation = yes to avoid constraining the input coordinates. 45: 45: Setting the LD random seed to -1220543294 45: Generated 8 of the 10 non-bonded parameter combinations 45: Excluding 2 bonded neighbours molecule type 'Methanol' 45: Excluding 2 bonded neighbours molecule type 'SOL' 45: Number of degrees of freedom in T-Coupling group rest is 12.00 45: 45: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 45: NVE simulation: will use the initial temperature of 1046.791 K for 45: determining the Verlet buffer size 45: 45: Estimate for the relative computational load of the PME mesh part: 1.00 45: 45: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 45: The optimal PME mesh load for parallel simulations is below 0.5 45: and for highly parallel simulations between 0.25 and 0.33, 45: for higher performance, increase the cut-off and the PME grid spacing. 45: 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc-and-methanol' 45: 0 steps, 0.0 ps. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.002 0.001 185.8 45: (ns/day) (hour/ns) 45: Performance: 74.920 0.320 45: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as double precision energy file 45: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 45: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 45: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: Calculating fourier grid dimensions for X Y Z 45: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 45: This run will generate roughly 0 Mb of data 45: [ OK ] PmeTest.ScalesTheBox (77 ms) 45: [ RUN ] PmeTest.ScalesTheBoxWithWalls 45: 45: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]: 45: For a correct single-point energy evaluation with nsteps = 0, use 45: continuation = yes to avoid constraining the input coordinates. 45: 45: Setting the LD random seed to -139515909 45: Generated 8 of the 10 non-bonded parameter combinations 45: Excluding 2 bonded neighbours molecule type 'Methanol' 45: Excluding 2 bonded neighbours molecule type 'SOL' 45: Searching the wall atom type(s) 45: Number of degrees of freedom in T-Coupling group rest is 13.00 45: 45: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]: 45: NVE simulation: will use the initial temperature of 966.268 K for 45: determining the Verlet buffer size 45: 45: Estimate for the relative computational load of the PME mesh part: 1.00 45: 45: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]: 45: The optimal PME mesh load for parallel simulations is below 0.5 45: and for highly parallel simulations between 0.25 and 0.33, 45: for higher performance, increase the cut-off and the PME grid spacing. 45: 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc-and-methanol' 45: 0 steps, 0.0 ps. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.024 0.012 197.6 45: (ns/day) (hour/ns) 45: Performance: 7.152 3.356 45: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as double precision energy file 45: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 45: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 45: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: Calculating fourier grid dimensions for X Y Z 45: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118 45: This run will generate roughly 0 Mb of data 45: [ OK ] PmeTest.ScalesTheBoxWithWalls (712 ms) 45: [----------] 3 tests from PmeTest (1205 ms total) 45: 45: [----------] 1 test from CompelTest 45: [ RUN ] CompelTest.SwapCanRun 45: 45: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 45: The Berendsen thermostat does not generate the correct kinetic energy 45: distribution. You might want to consider using the V-rescale thermostat. 45: 45: Setting the LD random seed to -1093281093 45: Generated 330891 of the 330891 non-bonded parameter combinations 45: Generating 1-4 interactions: fudge = 0.5 45: Generated 330891 of the 330891 1-4 parameter combinations 45: Excluding 3 bonded neighbours molecule type 'Protein' 45: Excluding 3 bonded neighbours molecule type 'OCT' 45: Excluding 1 bonded neighbours molecule type 'NA' 45: Excluding 1 bonded neighbours molecule type 'CL' 45: Excluding 3 bonded neighbours molecule type 'Protein' 45: Excluding 3 bonded neighbours molecule type 'OCT' 45: Excluding 2 bonded neighbours molecule type 'SOL' 45: Split0 group 'Ch0' contains 83 atoms. 45: Split1 group 'Ch1' contains 83 atoms. 45: Solvent group 'SOL' contains 11931 atoms. 45: Swap group 'NA+' contains 19 atoms. 45: Swap group 'CL-' contains 19 atoms. 45: Number of degrees of freedom in T-Coupling group System is 27869.00 45: 45: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 45: Removing center of mass motion in the presence of position restraints 45: might cause artifacts. When you are using position restraints to 45: equilibrate a macro-molecule, the artifacts are usually negligible. 45: 45: 45: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 45: You are using a plain Coulomb cut-off, which might produce artifacts. 45: You might want to consider using PME electrostatics. 45: 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: SWAP: Determining initial numbers of ions per compartment. 45: SWAP: Setting pointers for checkpoint writing 45: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 45: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 45: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 45: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 45: starting mdrun 'Channel_coco in octane membrane' 45: 2 steps, 0.0 ps. 45: turning all bonds into constraints... 45: turning all bonds into constraints... 45: turning all bonds into constraints... 45: turning all bonds into constraints... 45: turning all bonds into constraints... 45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 45: Calculated rlist for 1x1 atom pair-list as 1.314 nm, buffer size 0.314 nm 45: Set rlist, assuming 4x4 atom pair-list, to 1.260 nm, buffer size 0.260 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: This run will generate roughly 1 Mb of data 45: 45: Writing final coordinates. 45: 45: NOTE: 37 % of the run time was spent in pair search, 45: you might want to increase nstlist (this has no effect on accuracy) 45: 45: Core t (s) Wall t (s) (%) 45: Time: 1.400 0.700 200.0 45: (ns/day) (hour/ns) 45: Performance: 1.851 12.964 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: SWAP: Setting pointers for checkpoint writing 45: SWAP: Copying channel fluxes from checkpoint file data 45: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 45: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 45: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 45: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 45: starting mdrun 'Channel_coco in octane membrane' 45: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 45: 45: Writing final coordinates. 45: 45: NOTE: 21 % of the run time was spent in pair search, 45: you might want to increase nstlist (this has no effect on accuracy) 45: 45: Core t (s) Wall t (s) (%) 45: Time: 1.000 0.500 199.9 45: (ns/day) (hour/ns) 45: Performance: 2.592 9.260 45: [ OK ] CompelTest.SwapCanRun (2299 ms) 45: [----------] 1 test from CompelTest (2299 ms total) 45: 45: [----------] 6 tests from BondedInteractionsTest 45: [ RUN ] BondedInteractionsTest.NormalBondWorks 45: 45: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 45: For a correct single-point energy evaluation with nsteps = 0, use 45: continuation = yes to avoid constraining the input coordinates. 45: 45: Setting the LD random seed to 1312169983 45: Generated 3 of the 3 non-bonded parameter combinations 45: Excluding 3 bonded neighbours molecule type 'butane' 45: 45: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 45: In moleculetype 'butane' 2 atoms are not bound by a potential or 45: constraint to any other atom in the same moleculetype. Although 45: technically this might not cause issues in a simulation, this often means 45: that the user forgot to add a bond/potential/constraint or put multiple 45: molecules in the same moleculetype definition by mistake. Run with -v to 45: get information for each atom. 45: 45: Number of degrees of freedom in T-Coupling group rest is 9.00 45: 45: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 45: NVE simulation with an initial temperature of zero: will use a Verlet 45: buffer of 10%. Check your energy drift! 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/butane1.gro' 45: 45: Reading frames from gro file 'A single butane', 4 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: 45: NOTE: 25 % of the run time was spent in pair search, 45: you might want to increase nstlist (this has no effect on accuracy) 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.001 0.000 189.7 45: (ns/day) (hour/ns) 45: Performance: 230.673 0.104 45: This run will generate roughly 0 Mb of data 45: [ OK ] BondedInteractionsTest.NormalBondWorks (8 ms) 45: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 45: 45: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 45: For a correct single-point energy evaluation with nsteps = 0, use 45: continuation = yes to avoid constraining the input coordinates. 45: 45: Setting the LD random seed to -261 45: Generated 3 of the 3 non-bonded parameter combinations 45: Excluding 3 bonded neighbours molecule type 'butane' 45: 45: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 45: In moleculetype 'butane' 2 atoms are not bound by a potential or 45: constraint to any other atom in the same moleculetype. Although 45: technically this might not cause issues in a simulation, this often means 45: that the user forgot to add a bond/potential/constraint or put multiple 45: molecules in the same moleculetype definition by mistake. Run with -v to 45: get information for each atom. 45: 45: Number of degrees of freedom in T-Coupling group rest is 9.00 45: 45: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 45: NVE simulation with an initial temperature of zero: will use a Verlet 45: buffer of 10%. Check your energy drift! 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/butane1.gro' 45: 45: Reading frames from gro file 'A single butane', 4 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: 45: NOTE: 17 % of the run time was spent in pair search, 45: you might want to increase nstlist (this has no effect on accuracy) 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.001 0.000 186.9 45: (ns/day) (hour/ns) 45: Performance: 260.149 0.092 45: This run will generate roughly 0 Mb of data 45: [ OK ] BondedInteractionsTest.TabulatedBondWorks (16 ms) 45: [ RUN ] BondedInteractionsTest.NormalAngleWorks 45: 45: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 45: For a correct single-point energy evaluation with nsteps = 0, use 45: continuation = yes to avoid constraining the input coordinates. 45: 45: Setting the LD random seed to 208334842 45: Generated 3 of the 3 non-bonded parameter combinations 45: Excluding 3 bonded neighbours molecule type 'butane' 45: 45: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 45: In moleculetype 'butane' 4 atoms are not bound by a potential or 45: constraint to any other atom in the same moleculetype. Although 45: technically this might not cause issues in a simulation, this often means 45: that the user forgot to add a bond/potential/constraint or put multiple 45: molecules in the same moleculetype definition by mistake. Run with -v to 45: get information for each atom. 45: 45: Number of degrees of freedom in T-Coupling group rest is 9.00 45: 45: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 45: NVE simulation with an initial temperature of zero: will use a Verlet 45: buffer of 10%. Check your energy drift! 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/butane1.gro' 45: 45: Reading frames from gro file 'A single butane', 4 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: 45: NOTE: 16 % of the run time was spent in pair search, 45: you might want to increase nstlist (this has no effect on accuracy) 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.001 0.000 187.3 45: (ns/day) (hour/ns) 45: Performance: 265.097 0.091 45: This run will generate roughly 0 Mb of data 45: [ OK ] BondedInteractionsTest.NormalAngleWorks (8 ms) 45: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 45: 45: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 45: For a correct single-point energy evaluation with nsteps = 0, use 45: continuation = yes to avoid constraining the input coordinates. 45: 45: Setting the LD random seed to -59507715 45: Generated 3 of the 3 non-bonded parameter combinations 45: Excluding 3 bonded neighbours molecule type 'butane' 45: 45: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 45: In moleculetype 'butane' 4 atoms are not bound by a potential or 45: constraint to any other atom in the same moleculetype. Although 45: technically this might not cause issues in a simulation, this often means 45: that the user forgot to add a bond/potential/constraint or put multiple 45: molecules in the same moleculetype definition by mistake. Run with -v to 45: get information for each atom. 45: 45: Number of degrees of freedom in T-Coupling group rest is 9.00 45: 45: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 45: NVE simulation with an initial temperature of zero: will use a Verlet 45: buffer of 10%. Check your energy drift! 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/butane1.gro' 45: 45: Reading frames from gro file 'A single butane', 4 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: 45: NOTE: 18 % of the run time was spent in pair search, 45: you might want to increase nstlist (this has no effect on accuracy) 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.001 0.000 190.0 45: (ns/day) (hour/ns) 45: Performance: 216.739 0.111 45: This run will generate roughly 0 Mb of data 45: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (8 ms) 45: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 45: 45: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 45: For a correct single-point energy evaluation with nsteps = 0, use 45: continuation = yes to avoid constraining the input coordinates. 45: 45: Setting the LD random seed to -438321507 45: Generated 3 of the 3 non-bonded parameter combinations 45: Excluding 3 bonded neighbours molecule type 'butane' 45: 45: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 45: In moleculetype 'butane' 4 atoms are not bound by a potential or 45: constraint to any other atom in the same moleculetype. Although 45: technically this might not cause issues in a simulation, this often means 45: that the user forgot to add a bond/potential/constraint or put multiple 45: molecules in the same moleculetype definition by mistake. Run with -v to 45: get information for each atom. 45: 45: Number of degrees of freedom in T-Coupling group rest is 9.00 45: 45: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 45: NVE simulation with an initial temperature of zero: will use a Verlet 45: buffer of 10%. Check your energy drift! 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/butane1.gro' 45: 45: Reading frames from gro file 'A single butane', 4 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: 45: NOTE: 15 % of the run time was spent in pair search, 45: you might want to increase nstlist (this has no effect on accuracy) 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.001 0.000 187.0 45: (ns/day) (hour/ns) 45: Performance: 238.413 0.101 45: This run will generate roughly 0 Mb of data 45: [ OK ] BondedInteractionsTest.NormalDihedralWorks (6 ms) 45: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 45: 45: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 45: For a correct single-point energy evaluation with nsteps = 0, use 45: continuation = yes to avoid constraining the input coordinates. 45: 45: Setting the LD random seed to -833 45: Generated 3 of the 3 non-bonded parameter combinations 45: Excluding 3 bonded neighbours molecule type 'butane' 45: 45: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 45: In moleculetype 'butane' 4 atoms are not bound by a potential or 45: constraint to any other atom in the same moleculetype. Although 45: technically this might not cause issues in a simulation, this often means 45: that the user forgot to add a bond/potential/constraint or put multiple 45: molecules in the same moleculetype definition by mistake. Run with -v to 45: get information for each atom. 45: 45: Number of degrees of freedom in T-Coupling group rest is 9.00 45: 45: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 45: NVE simulation with an initial temperature of zero: will use a Verlet 45: buffer of 10%. Check your energy drift! 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/butane1.gro' 45: 45: Reading frames from gro file 'A single butane', 4 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: 45: NOTE: 16 % of the run time was spent in pair search, 45: you might want to increase nstlist (this has no effect on accuracy) 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.001 0.000 187.0 45: (ns/day) (hour/ns) 45: Performance: 287.154 0.084 45: This run will generate roughly 0 Mb of data 45: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (22 ms) 45: [----------] 6 tests from BondedInteractionsTest (68 ms total) 45: 45: [----------] 4 tests from SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest 45: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/0 45: 45: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 45: that with the Verlet scheme, nstlist has no effect on the accuracy of 45: your simulation. 45: 45: 45: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 45: Setting nstcalcenergy (100) equal to nstenergy (4) 45: 45: Generated 1 of the 1 non-bonded parameter combinations 45: Excluding 1 bonded neighbours molecule type 'Argon' 45: Number of degrees of freedom in T-Coupling group System is 33.00 45: 45: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 45: NVE simulation: will use the initial temperature of 68.810 K for 45: determining the Verlet buffer size 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'Argon' 45: 16 steps, 0.0 ps. 45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 45: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 45: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: This run will generate roughly 0 Mb of data 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.014 0.007 198.3 45: (ns/day) (hour/ns) 45: Performance: 207.016 0.116 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'Argon' 45: 16 steps, 0.0 ps. 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.008 0.004 196.4 45: (ns/day) (hour/ns) 45: Performance: 356.104 0.067 45: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 45: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 45: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 trr version: GMX_trn_file (double precision) 45: 45: 45: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/0 (44 ms) 45: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/1 45: 45: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 45: that with the Verlet scheme, nstlist has no effect on the accuracy of 45: your simulation. 45: 45: 45: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 45: Setting nstcalcenergy (100) equal to nstenergy (4) 45: 45: Generated 1 of the 1 non-bonded parameter combinations 45: Excluding 1 bonded neighbours molecule type 'Argon' 45: Number of degrees of freedom in T-Coupling group System is 33.00 45: 45: There were 2 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 45: 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'Argon' 45: 16 steps, 0.0 ps. 45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 45: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 45: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: This run will generate roughly 0 Mb of data 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.009 0.005 198.3 45: (ns/day) (hour/ns) 45: Performance: 307.323 0.078 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 45: 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'Argon' 45: 16 steps, 0.0 ps. 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.008 0.004 196.4 45: (ns/day) (hour/ns) 45: Performance: 364.597 0.066 45: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 45: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 45: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 45: 45: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/1 (25 ms) 45: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/2 45: 45: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 45: that with the Verlet scheme, nstlist has no effect on the accuracy of 45: your simulation. 45: 45: 45: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 45: Setting nstcalcenergy (100) equal to nstenergy (4) 45: 45: Generated 330891 of the 330891 non-bonded parameter combinations 45: Generating 1-4 interactions: fudge = 0.5 45: Generated 330891 of the 330891 1-4 parameter combinations 45: Excluding 2 bonded neighbours molecule type 'SOL' 45: Number of degrees of freedom in T-Coupling group System is 27.00 45: 45: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 45: NVE simulation: will use the initial temperature of 398.997 K for 45: determining the Verlet buffer size 45: 45: 45: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 45: You are using a plain Coulomb cut-off, which might produce artifacts. 45: You might want to consider using PME electrostatics. 45: 45: 45: 45: There were 4 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc2' 45: 16 steps, 0.0 ps. 45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 45: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 45: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: This run will generate roughly 0 Mb of data 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.075 0.037 199.7 45: (ns/day) (hour/ns) 45: Performance: 39.325 0.610 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc2' 45: 16 steps, 0.0 ps. 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.019 0.009 197.9 45: (ns/day) (hour/ns) 45: Performance: 155.151 0.155 45: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim2.edr as double precision energy file 45: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim1.edr as double precision energy file 45: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 45: 45: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/2 (767 ms) 45: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/3 45: 45: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_input.mdp]: 45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 45: that with the Verlet scheme, nstlist has no effect on the accuracy of 45: your simulation. 45: 45: 45: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_input.mdp]: 45: Setting nstcalcenergy (100) equal to nstenergy (4) 45: 45: Generated 330891 of the 330891 non-bonded parameter combinations 45: Generating 1-4 interactions: fudge = 0.5 45: Generated 330891 of the 330891 1-4 parameter combinations 45: Excluding 2 bonded neighbours molecule type 'SOL' 45: Number of degrees of freedom in T-Coupling group System is 27.00 45: 45: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_input.mdp]: 45: You are using a plain Coulomb cut-off, which might produce artifacts. 45: You might want to consider using PME electrostatics. 45: 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 45: 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc2' 45: 16 steps, 0.0 ps. 45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 45: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 45: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: This run will generate roughly 0 Mb of data 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.010 0.005 198.1 45: (ns/day) (hour/ns) 45: Performance: 298.233 0.080 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 45: 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc2' 45: 16 steps, 0.0 ps. 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.009 0.005 195.0 45: (ns/day) (hour/ns) 45: Performance: 325.888 0.074 45: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_sim2.edr as double precision energy file 45: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_sim1.edr as double precision energy file 45: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 45: 45: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/3 (635 ms) 45: [----------] 4 tests from SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest (1471 ms total) 45: 45: [----------] 8 tests from SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest 45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/0 45: 45: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 45: that with the Verlet scheme, nstlist has no effect on the accuracy of 45: your simulation. 45: 45: 45: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 45: Setting nstcalcenergy (100) equal to nstenergy (4) 45: 45: Generated 1 of the 1 non-bonded parameter combinations 45: Excluding 1 bonded neighbours molecule type 'Argon' 45: Number of degrees of freedom in T-Coupling group System is 33.00 45: 45: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 45: NVE simulation: will use the initial temperature of 68.810 K for 45: determining the Verlet buffer size 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'Argon' 45: 16 steps, 0.0 ps. 45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 45: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 45: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: This run will generate roughly 0 Mb of data 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.020 0.010 198.1 45: (ns/day) (hour/ns) 45: Performance: 144.795 0.166 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'Argon' 45: 16 steps, 0.0 ps. 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.018 0.009 199.1 45: (ns/day) (hour/ns) 45: Performance: 164.418 0.146 45: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 45: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 45: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 45: 45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/0 (75 ms) 45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/1 45: 45: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 45: that with the Verlet scheme, nstlist has no effect on the accuracy of 45: your simulation. 45: 45: 45: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 45: Setting nstcalcenergy (100) equal to nstenergy (4) 45: 45: Generated 1 of the 1 non-bonded parameter combinations 45: Excluding 1 bonded neighbours molecule type 'Argon' 45: Number of degrees of freedom in T-Coupling group System is 33.00 45: 45: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 45: NVE simulation: will use the initial temperature of 68.810 K for 45: determining the Verlet buffer size 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'Argon' 45: 16 steps, 0.0 ps. 45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 45: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 45: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: This run will generate roughly 0 Mb of data 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.007 0.004 196.6 45: (ns/day) (hour/ns) 45: Performance: 398.976 0.060 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'Argon' 45: 16 steps, 0.0 ps. 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.008 0.004 198.3 45: (ns/day) (hour/ns) 45: Performance: 366.201 0.066 45: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 45: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 45: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 45: 45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/1 (21 ms) 45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/2 45: 45: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 45: that with the Verlet scheme, nstlist has no effect on the accuracy of 45: your simulation. 45: 45: 45: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 45: Setting nstcalcenergy (100) equal to nstenergy (4) 45: 45: Generated 1 of the 1 non-bonded parameter combinations 45: Excluding 1 bonded neighbours molecule type 'Argon' 45: Number of degrees of freedom in T-Coupling group System is 33.00 45: 45: There were 2 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 45: 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'Argon' 45: 16 steps, 0.0 ps. 45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 45: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 45: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: This run will generate roughly 0 Mb of data 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.007 0.004 197.8 45: (ns/day) (hour/ns) 45: Performance: 400.194 0.060 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 45: 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'Argon' 45: 16 steps, 0.0 ps. 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.015 0.008 198.8 45: (ns/day) (hour/ns) 45: Performance: 188.582 0.127 45: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim2.edr as double precision energy file 45: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim1.edr as double precision energy file 45: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 45: 45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/2 (63 ms) 45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/3 45: 45: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_input.mdp]: 45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 45: that with the Verlet scheme, nstlist has no effect on the accuracy of 45: your simulation. 45: 45: 45: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_input.mdp]: 45: Setting nstcalcenergy (100) equal to nstenergy (4) 45: 45: Generated 1 of the 1 non-bonded parameter combinations 45: Excluding 1 bonded neighbours molecule type 'Argon' 45: Number of degrees of freedom in T-Coupling group System is 33.00 45: 45: There were 2 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 45: 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'Argon' 45: 16 steps, 0.0 ps. 45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 45: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 45: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: This run will generate roughly 0 Mb of data 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.011 0.006 196.2 45: (ns/day) (hour/ns) 45: Performance: 253.064 0.095 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 45: 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'Argon' 45: 16 steps, 0.0 ps. 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.010 0.005 198.2 45: (ns/day) (hour/ns) 45: Performance: 283.480 0.085 45: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_sim2.edr as double precision energy file 45: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_sim1.edr as double precision energy file 45: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 45: 45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/3 (88 ms) 45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/4 45: 45: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]: 45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 45: that with the Verlet scheme, nstlist has no effect on the accuracy of 45: your simulation. 45: 45: 45: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]: 45: Setting nstcalcenergy (100) equal to nstenergy (4) 45: 45: Generated 330891 of the 330891 non-bonded parameter combinations 45: Generating 1-4 interactions: fudge = 0.5 45: Generated 330891 of the 330891 1-4 parameter combinations 45: Excluding 2 bonded neighbours molecule type 'SOL' 45: Number of degrees of freedom in T-Coupling group System is 27.00 45: 45: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]: 45: NVE simulation: will use the initial temperature of 398.997 K for 45: determining the Verlet buffer size 45: 45: 45: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]: 45: You are using a plain Coulomb cut-off, which might produce artifacts. 45: You might want to consider using PME electrostatics. 45: 45: 45: 45: There were 4 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc2' 45: 16 steps, 0.0 ps. 45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 45: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 45: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: This run will generate roughly 0 Mb of data 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.197 0.099 199.9 45: (ns/day) (hour/ns) 45: Performance: 14.882 1.613 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc2' 45: 16 steps, 0.0 ps. 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.024 0.012 199.4 45: (ns/day) (hour/ns) 45: Performance: 120.003 0.200 45: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim2.edr as double precision energy file 45: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim1.edr as double precision energy file 45: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 45: 45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/4 (916 ms) 45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/5 45: 45: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]: 45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 45: that with the Verlet scheme, nstlist has no effect on the accuracy of 45: your simulation. 45: 45: 45: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]: 45: Setting nstcalcenergy (100) equal to nstenergy (4) 45: 45: Generated 330891 of the 330891 non-bonded parameter combinations 45: Generating 1-4 interactions: fudge = 0.5 45: Generated 330891 of the 330891 1-4 parameter combinations 45: Excluding 2 bonded neighbours molecule type 'SOL' 45: Number of degrees of freedom in T-Coupling group System is 27.00 45: 45: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]: 45: NVE simulation: will use the initial temperature of 398.997 K for 45: determining the Verlet buffer size 45: 45: 45: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]: 45: You are using a plain Coulomb cut-off, which might produce artifacts. 45: You might want to consider using PME electrostatics. 45: 45: 45: 45: There were 4 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc2' 45: 16 steps, 0.0 ps. 45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 45: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 45: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: This run will generate roughly 0 Mb of data 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.029 0.015 198.8 45: (ns/day) (hour/ns) 45: Performance: 100.512 0.239 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Can not increase nstlist because an NVE ensemble is used 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc2' 45: 16 steps, 0.0 ps. 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.016 0.008 198.9 45: (ns/day) (hour/ns) 45: Performance: 180.779 0.133 45: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim2.edr as double precision energy file 45: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim1.edr as double precision energy file 45: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 45: 45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/5 (747 ms) 45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/6 45: 45: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 45: that with the Verlet scheme, nstlist has no effect on the accuracy of 45: your simulation. 45: 45: 45: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 45: Setting nstcalcenergy (100) equal to nstenergy (4) 45: 45: Generated 330891 of the 330891 non-bonded parameter combinations 45: Generating 1-4 interactions: fudge = 0.5 45: Generated 330891 of the 330891 1-4 parameter combinations 45: Excluding 2 bonded neighbours molecule type 'SOL' 45: Number of degrees of freedom in T-Coupling group System is 27.00 45: 45: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 45: You are using a plain Coulomb cut-off, which might produce artifacts. 45: You might want to consider using PME electrostatics. 45: 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 45: 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc2' 45: 16 steps, 0.0 ps. 45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 45: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 45: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: This run will generate roughly 0 Mb of data 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.024 0.012 198.3 45: (ns/day) (hour/ns) 45: Performance: 121.095 0.198 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 45: 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc2' 45: 16 steps, 0.0 ps. 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.023 0.012 199.2 45: (ns/day) (hour/ns) 45: Performance: 127.335 0.188 45: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim2.edr as double precision energy file 45: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim1.edr as double precision energy file 45: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 45: 45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/6 (688 ms) 45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/7 45: 45: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 45: that with the Verlet scheme, nstlist has no effect on the accuracy of 45: your simulation. 45: 45: 45: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 45: Setting nstcalcenergy (100) equal to nstenergy (4) 45: 45: Generated 330891 of the 330891 non-bonded parameter combinations 45: Generating 1-4 interactions: fudge = 0.5 45: Generated 330891 of the 330891 1-4 parameter combinations 45: Excluding 2 bonded neighbours molecule type 'SOL' 45: Number of degrees of freedom in T-Coupling group System is 27.00 45: 45: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 45: You are using a plain Coulomb cut-off, which might produce artifacts. 45: You might want to consider using PME electrostatics. 45: 45: 45: 45: There were 3 notes 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 45: 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc2' 45: 16 steps, 0.0 ps. 45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 45: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 45: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 45: Note that mdrun will redetermine rlist based on the actual pair-list setup 45: This run will generate roughly 0 Mb of data 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.034 0.017 199.0 45: (ns/day) (hour/ns) 45: Performance: 84.889 0.283 45: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 45: log). 45: The current CPU can measure timings more accurately than the code in 45: mdrun-test was configured to use. This might affect your simulation 45: speed as accurate timings are needed for load-balancing. 45: Please consider rebuilding mdrun-test with the GMX_USE_RDTSCP=ON CMake option. 45: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 45: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 45: 45: 45: Using 1 MPI thread 45: 45: Non-default thread affinity set, disabling internal thread affinity 45: 45: Using 2 OpenMP threads 45: 45: starting mdrun 'spc2' 45: 16 steps, 0.0 ps. 45: 45: Writing final coordinates. 45: 45: Core t (s) Wall t (s) (%) 45: Time: 0.007 0.004 198.3 45: (ns/day) (hour/ns) 45: Performance: 412.273 0.058 45: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim2.edr as double precision energy file 45: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim1.edr as double precision energy file 45: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 45: 45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/7 (696 ms) 45: [----------] 8 tests from SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest (3294 ms total) 45: 45: [----------] Global test environment tear-down 45: [==========] 24 tests from 7 test cases ran. (9010 ms total) 45: [ PASSED ] 24 tests. 45/54 Test #45: MdrunTests .......................... Passed 9.04 sec test 46 Start 46: MdrunNonIntegratorTests 46: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/MdrunNonIntegratorTests.xml" 46: Test timeout computed to be: 600 46: [==========] Running 65 tests from 7 test cases. 46: [----------] Global test environment set-up. 46: [----------] 1 test from NonbondedBenchTest 46: [ RUN ] NonbondedBenchTest.BasicEndToEndTest 46: SIMD width: 2 46: System size: 3000 atoms 46: Cut-off radius: 1 nm 46: Number of threads: 1 46: Number of iterations: 1 46: Compute energies: no 46: Ewald excl. corr.: analytical 46: 46: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle 46: total useful 46: Ewald all geom. 4xM 118.414 118.4143 0.0089 0.0053 46: [ OK ] NonbondedBenchTest.BasicEndToEndTest (87 ms) 46: [----------] 1 test from NonbondedBenchTest (87 ms total) 46: 46: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 330891 of the 330891 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 330891 of the 330891 1-4 parameter combinations 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 27.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Steepest Descents: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: 46: Energy minimization reached the maximum number of steps before the forces 46: reached the requested precision Fmax < 10. 46: 46: writing lowest energy coordinates. 46: 46: Steepest Descents did not converge to Fmax < 10 in 5 steps. 46: Potential Energy = -4.79910463671045e+01 46: Maximum force = 1.86297359432218e+02 on atom 13 46: Norm of force = 8.77219865482098e+01 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (675 ms) 46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 330891 of the 330891 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 330891 of the 330891 1-4 parameter combinations 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 27.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Polak-Ribiere Conjugate Gradients: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: F-max = 3.02331e+02 on atom 3 46: F-Norm = 1.18024e+02 46: 46: 46: Energy minimization reached the maximum number of steps before the forces 46: reached the requested precision Fmax < 10. 46: 46: writing lowest energy coordinates. 46: 46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 46: Potential Energy = -5.58622538633253e+01 46: Maximum force = 4.27274822366642e+02 on atom 13 46: Norm of force = 1.84530029253881e+02 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (791 ms) 46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 20503 of the 20503 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 1 46: Generated 17396 of the 20503 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Glycine' 46: Number of degrees of freedom in T-Coupling group System is 22.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Steepest Descents: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: 46: Energy minimization reached the maximum number of steps before the forces 46: reached the requested precision Fmax < 10. 46: 46: writing lowest energy coordinates. 46: 46: Steepest Descents did not converge to Fmax < 10 in 5 steps. 46: Potential Energy = 3.19376899751521e+02 46: Maximum force = 9.99884921009767e+03 on atom 9 46: Norm of force = 4.61669565054298e+03 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 turning H bonds into constraints... 46: This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (269 ms) 46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 20503 of the 20503 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 1 46: Generated 17396 of the 20503 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Glycine' 46: 46: NOTE 3 [file glycine_vacuo.top, line 12]: 46: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 46: 46: Number of degrees of freedom in T-Coupling group System is 22.00 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Polak-Ribiere Conjugate Gradients: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: F-max = 2.41575e+04 on atom 10 46: F-Norm = 1.18451e+04 46: 46: 46: Energy minimization reached the maximum number of steps before the forces 46: reached the requested precision Fmax < 10. 46: 46: writing lowest energy coordinates. 46: 46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 46: Potential Energy = 1.51743018140930e+02 46: Maximum force = 7.42089573409109e+03 on atom 9 46: Norm of force = 3.56929298615740e+03 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 turning H bonds into constraints... 46: This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (242 ms) 46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 2145 of the 2145 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2145 of the 2145 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 46: 46: NOTE 3 [file unknown]: 46: You are using constraints on all bonds, whereas the forcefield has been 46: parametrized only with constraints involving hydrogen atoms. We suggest 46: using constraints = h-bonds instead, this will also improve performance. 46: 46: Cleaning up constraints and constant bonded interactions with virtual sites 46: Removed 18 Angles with virtual sites, 21 left 46: Removed 10 Proper Dih.s with virtual sites, 44 left 46: Converted 15 Constraints with virtual sites to connections, 7 left 46: Number of degrees of freedom in T-Coupling group System is 23.00 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Steepest Descents: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: 46: Energy minimization reached the maximum number of steps before the forces 46: reached the requested precision Fmax < 10. 46: 46: writing lowest energy coordinates. 46: 46: Steepest Descents did not converge to Fmax < 10 in 5 steps. 46: Potential Energy = -1.56984193848274e+02 46: Maximum force = 4.56923624626205e+02 on atom 17 46: Norm of force = 1.83258377168315e+02 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 turning all bonds into constraints... 46: This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (24 ms) 46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 2145 of the 2145 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2145 of the 2145 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 46: 46: NOTE 3 [file unknown]: 46: You are using constraints on all bonds, whereas the forcefield has been 46: parametrized only with constraints involving hydrogen atoms. We suggest 46: using constraints = h-bonds instead, this will also improve performance. 46: 46: 46: NOTE 4 [file unknown]: 46: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 46: 46: Cleaning up constraints and constant bonded interactions with virtual sites 46: Removed 18 Angles with virtual sites, 21 left 46: Removed 10 Proper Dih.s with virtual sites, 44 left 46: Converted 15 Constraints with virtual sites to connections, 7 left 46: Number of degrees of freedom in T-Coupling group System is 23.00 46: 46: NOTE 5 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 5 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Polak-Ribiere Conjugate Gradients: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: F-max = 1.06800e+03 on atom 28 46: F-Norm = 4.26922e+02 46: 46: 46: Energy minimization reached the maximum number of steps before the forces 46: reached the requested precision Fmax < 10. 46: 46: writing lowest energy coordinates. 46: 46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 46: Potential Energy = -1.69410778678182e+02 46: Maximum force = 2.18225948474131e+02 on atom 17 46: Norm of force = 7.92068036537818e+01 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 turning all bonds into constraints... 46: This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (18 ms) 46: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (2020 ms total) 46: 46: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 1 of the 1 non-bonded parameter combinations 46: Excluding 1 bonded neighbours molecule type 'Argon' 46: Number of degrees of freedom in T-Coupling group System is 33.00 46: 46: There were 2 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Steepest Descents: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: 46: writing lowest energy coordinates. 46: 46: Steepest Descents converged to Fmax < 10 in 1 steps 46: Potential Energy = -9.74257075835447e-01 46: Maximum force = 4.01322929015133e+00 on atom 1 46: Norm of force = 1.63839399694378e+00 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (5 ms) 46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 1 of the 1 non-bonded parameter combinations 46: Excluding 1 bonded neighbours molecule type 'Argon' 46: Number of degrees of freedom in T-Coupling group System is 33.00 46: 46: There were 2 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Polak-Ribiere Conjugate Gradients: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: F-max = 4.01323e+00 on atom 1 46: F-Norm = 1.63839e+00 46: 46: 46: writing lowest energy coordinates. 46: 46: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 46: Potential Energy = -9.90642313893957e-01 46: Maximum force = 2.57812909491105e+00 on atom 1 46: Norm of force = 1.05251679559258e+00 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (6 ms) 46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: 46: WARNING 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 46: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 46: 46: Generated 1 of the 1 non-bonded parameter combinations 46: Excluding 1 bonded neighbours molecule type 'Argon' 46: Number of degrees of freedom in T-Coupling group System is 33.00 46: 46: There were 2 notes 46: 46: There was 1 warning 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: 46: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Low-Memory BFGS Minimizer: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: Using 10 BFGS correction steps. 46: 46: F-max = 4.01323e+00 on atom 1 46: F-Norm = 1.63839e+00 46: 46: 46: writing lowest energy coordinates. 46: 46: Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps 46: Potential Energy = -9.90642313893957e-01 46: Maximum force = 2.57812909491105e+00 on atom 1 46: Norm of force = 1.05251679559258e+00 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (6 ms) 46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 20503 of the 20503 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 1 46: Generated 17396 of the 20503 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Glycine' 46: Number of degrees of freedom in T-Coupling group System is 27.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Steepest Descents: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: 46: Energy minimization reached the maximum number of steps before the forces 46: reached the requested precision Fmax < 10. 46: 46: writing lowest energy coordinates. 46: 46: Steepest Descents did not converge to Fmax < 10 in 5 steps. 46: Potential Energy = 3.19395484891520e+02 46: Maximum force = 9.97041707197911e+03 on atom 9 46: Norm of force = 4.62274878665467e+03 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (214 ms) 46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 20503 of the 20503 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 1 46: Generated 17396 of the 20503 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Glycine' 46: Number of degrees of freedom in T-Coupling group System is 27.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Polak-Ribiere Conjugate Gradients: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: F-max = 2.41672e+04 on atom 10 46: F-Norm = 1.19357e+04 46: 46: 46: Energy minimization reached the maximum number of steps before the forces 46: reached the requested precision Fmax < 10. 46: 46: writing lowest energy coordinates. 46: 46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 46: Potential Energy = 1.56258793899481e+02 46: Maximum force = 7.50181017480396e+03 on atom 9 46: Norm of force = 3.61390332564874e+03 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (185 ms) 46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: 46: WARNING 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 46: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 46: 46: Generated 20503 of the 20503 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 1 46: Generated 17396 of the 20503 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Glycine' 46: Number of degrees of freedom in T-Coupling group System is 27.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: 46: There was 1 warning 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: 46: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: 46: Low-Memory BFGS Minimizer: 46: Tolerance (Fmax) = 1.00000e+01 46: Number of steps = 4 46: Using 10 BFGS correction steps. 46: 46: F-max = 2.41672e+04 on atom 10 46: F-Norm = 1.19357e+04 46: 46: 46: Energy minimization reached the maximum number of steps before the forces 46: reached the requested precision Fmax < 10. 46: 46: writing lowest energy coordinates. 46: 46: Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps. 46: Potential Energy = 5.61116097794205e+02 46: Maximum force = 1.26854826291223e+04 on atom 10 46: Norm of force = 6.06436286976271e+03 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data 46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (206 ms) 46: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (623 ms total) 46: 46: [----------] 5 tests from NormalModesWorks/NormalModesTest 46: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/0 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 3 of the 3 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 3 of the 3 1-4 parameter combinations 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 15.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: Small system size (N=6), using full Hessian format. 46: Allocating Hessian memory... 46: 46: starting normal mode calculation '2 scaled waters' 46: 12 steps. 46: 46: Maximum force: 9.96989e-06 46: 46: 46: Writing Hessian... 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Reading double precision matrix generated by GROMACS 2020.6-Debian-2020.6-2 46: 46: Diagonalizing to find vectors 7 through 18... 46: Writing eigenvalues... 46: 46: Writing average structure & eigenvectors 7--18 to eigenvec.trr 46: This run will generate roughly 0 Mb of data 46: There are: 6 Atoms 46: Using begin = 7 and end = 18 46: Full matrix storage format, nrow=18, ncols=18 46: Writing eigenfrequencies - negative eigenvalues will be set to zero. 46: Cannot compute entropy when -first = 7 46: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/0 (10 ms) 46: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/1 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 20503 of the 20503 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 1 46: Generated 17396 of the 20503 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 46: 46: NOTE 3 [file villin.top, line 2452]: 46: System has non-zero total charge: -2.000000 46: Total charge should normally be an integer. See 46: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 46: for discussion on how close it should be to an integer. 46: 46: 46: 46: Number of degrees of freedom in T-Coupling group System is 765.00 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: Small system size (N=256), using full Hessian format. 46: Allocating Hessian memory... 46: 46: starting normal mode calculation 'AMYLOID BETA A4 PROTEIN' 46: 512 steps. 46: 46: Maximum force: 6.97568e-04 46: 46: 46: Writing Hessian... 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Reading double precision matrix generated by GROMACS 2020.6-Debian-2020.6-2 46: 46: Diagonalizing to find vectors 7 through 50... 46: Writing eigenvalues... 46: 46: Writing average structure & eigenvectors 7--50 to eigenvec.trr 46: This run will generate roughly 0 Mb of data 46: There are: 256 Atoms 46: Using begin = 7 and end = 50 46: Full matrix storage format, nrow=768, ncols=768 46: Writing eigenfrequencies - negative eigenvalues will be set to zero. 46: Cannot compute entropy when -first = 7 46: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/1 (4589 ms) 46: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/2 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 330891 of the 330891 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 330891 of the 330891 1-4 parameter combinations 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 15.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: Small system size (N=6), using full Hessian format. 46: Allocating Hessian memory... 46: 46: starting normal mode calculation 'flex spc dimer' 46: 12 steps. 46: 46: Maximum force: 3.36401e-04 46: 46: 46: Writing Hessian... 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Reading double precision matrix generated by GROMACS 2020.6-Debian-2020.6-2 46: 46: Diagonalizing to find vectors 7 through 18... 46: Writing eigenvalues... 46: 46: Writing average structure & eigenvectors 7--18 to eigenvec.trr 46: This run will generate roughly 0 Mb of data 46: There are: 6 Atoms 46: Using begin = 7 and end = 18 46: Full matrix storage format, nrow=18, ncols=18 46: Writing eigenfrequencies - negative eigenvalues will be set to zero. 46: Cannot compute entropy when -first = 7 46: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/2 (679 ms) 46: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/3 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 46: nstcomm to nstcalcenergy 46: 46: Generated 330891 of the 330891 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 330891 of the 330891 1-4 parameter combinations 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Cleaning up constraints and constant bonded interactions with virtual sites 46: Number of degrees of freedom in T-Coupling group System is 6.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: Small system size (N=3), using full Hessian format. 46: Allocating Hessian memory... 46: 46: starting normal mode calculation '1 TIP5P' 46: 6 steps. 46: 46: Maximum force: 2.42882e-04 46: 46: 46: Writing Hessian... 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Reading double precision matrix generated by GROMACS 2020.6-Debian-2020.6-2 46: 46: Diagonalizing to find vectors 7 through 9... 46: Writing eigenvalues... 46: 46: Writing average structure & eigenvectors 7--9 to eigenvec.trr 46: This run will generate roughly 0 Mb of data 46: There are: 3 Atoms 46: There are: 2 VSites 46: Using begin = 7 and end = 9 46: Full matrix storage format, nrow=9, ncols=9 46: Writing eigenfrequencies - negative eigenvalues will be set to zero. 46: Cannot compute entropy when -first = 7 46: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/3 (1083 ms) 46: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/4 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: Generated 6 of the 10 non-bonded parameter combinations 46: Excluding 2 bonded neighbours molecule type 'SW' 46: Cleaning up constraints and constant bonded interactions with virtual sites 46: Number of degrees of freedom in T-Coupling group System is 15.00 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 2 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: Small system size (N=6), using full Hessian format. 46: Allocating Hessian memory... 46: 46: starting normal mode calculation 'sw dimer' 46: 12 steps. 46: 46: Maximum force: 1.07599e-03 46: The force is probably not small enough to ensure that you are at a minimum. 46: Be aware that negative eigenvalues may occur 46: when the resulting matrix is diagonalized. 46: 46: 46: Writing Hessian... 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Reading double precision matrix generated by GROMACS 2020.6-Debian-2020.6-2 46: 46: Diagonalizing to find vectors 7 through 18... 46: Writing eigenvalues... 46: 46: Writing average structure & eigenvectors 7--18 to eigenvec.trr 46: This run will generate roughly 0 Mb of data 46: There are: 6 Atoms 46: There are: 2 Shells 46: There are: 2 VSites 46: 46: NOTE: in the current version shell prediction during the crun is disabled 46: 46: Using begin = 7 and end = 18 46: Full matrix storage format, nrow=18, ncols=18 46: Writing eigenfrequencies - negative eigenvalues will be set to zero. 46: Cannot compute entropy when -first = 7 46: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/4 (16 ms) 46: [----------] 5 tests from NormalModesWorks/NormalModesTest (6378 ms total) 46: 46: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 1 of the 1 non-bonded parameter combinations 46: Excluding 1 bonded neighbours molecule type 'Argon' 46: Number of degrees of freedom in T-Coupling group System is 33.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 46: NVE simulation: will use the initial temperature of 68.810 K for 46: determining the Verlet buffer size 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'Argon' 46: 16 steps, 0.0 ps. 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 46: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.008 0.004 197.6 46: (ns/day) (hour/ns) 46: Performance: 353.245 0.068 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'Argon', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr' 46: 46: trr version: GMX_trn_file (double precision) 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 15 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.001 0.001 194.4 46: (ns/day) (hour/ns) 46: Performance: 2462.268 0.010 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (13 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 1 of the 1 non-bonded parameter combinations 46: Excluding 1 bonded neighbours molecule type 'Argon' 46: Number of degrees of freedom in T-Coupling group System is 33.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 46: NVE simulation: will use the initial temperature of 68.810 K for 46: determining the Verlet buffer size 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'Argon' 46: 16 steps, 0.0 ps. 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 46: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.008 0.004 198.2 46: (ns/day) (hour/ns) 46: Performance: 372.692 0.064 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'Argon', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 17 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.002 0.001 194.8 46: (ns/day) (hour/ns) 46: Performance: 1688.759 0.014 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (16 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 1 of the 1 non-bonded parameter combinations 46: Excluding 1 bonded neighbours molecule type 'Argon' 46: Number of degrees of freedom in T-Coupling group System is 33.00 46: 46: There were 2 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'Argon' 46: 16 steps, 0.0 ps. 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 46: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.006 0.003 197.2 46: (ns/day) (hour/ns) 46: Performance: 446.161 0.054 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'Argon', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 21 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.001 0.001 195.0 46: (ns/day) (hour/ns) 46: Performance: 2247.572 0.011 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (54 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 1 of the 1 non-bonded parameter combinations 46: Excluding 1 bonded neighbours molecule type 'Argon' 46: Number of degrees of freedom in T-Coupling group System is 33.00 46: 46: There were 2 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'Argon' 46: 16 steps, 0.0 ps. 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 46: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.009 0.004 196.8 46: (ns/day) (hour/ns) 46: Performance: 330.203 0.073 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'Argon', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 21 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.001 0.001 194.8 46: (ns/day) (hour/ns) 46: Performance: 2060.399 0.012 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (17 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 330891 of the 330891 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 330891 of the 330891 1-4 parameter combinations 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 27.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 46: NVE simulation: will use the initial temperature of 398.997 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'spc2' 46: 16 steps, 0.0 ps. 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 46: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.069 0.035 199.3 46: (ns/day) (hour/ns) 46: Performance: 42.356 0.567 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'spc2', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 18 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.002 0.001 194.9 46: (ns/day) (hour/ns) 46: Performance: 1788.790 0.013 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (593 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 330891 of the 330891 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 330891 of the 330891 1-4 parameter combinations 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 27.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 46: NVE simulation: will use the initial temperature of 398.997 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'spc2' 46: 16 steps, 0.0 ps. 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 46: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.008 0.004 198.5 46: (ns/day) (hour/ns) 46: Performance: 361.495 0.066 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'spc2', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 23 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.002 0.001 196.3 46: (ns/day) (hour/ns) 46: Performance: 1274.957 0.019 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (628 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 330891 of the 330891 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 330891 of the 330891 1-4 parameter combinations 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 27.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 100, rlist from 0.734 to 0.826 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'spc2' 46: 16 steps, 0.0 ps. 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.735 nm, buffer size 0.035 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.733 nm, buffer size 0.033 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.359 0.180 199.9 46: (ns/day) (hour/ns) 46: Performance: 8.173 2.936 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 100, rlist from 0.734 to 0.826 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'spc2', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 12 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 196.3 46: (ns/day) (hour/ns) 46: Performance: 997.344 0.024 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (799 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 330891 of the 330891 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 330891 of the 330891 1-4 parameter combinations 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 27.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'spc2' 46: 16 steps, 0.0 ps. 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.071 0.035 199.5 46: (ns/day) (hour/ns) 46: Performance: 41.534 0.578 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'spc2', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 10 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.005 0.002 197.2 46: (ns/day) (hour/ns) 46: Performance: 615.198 0.039 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (773 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2145 of the 2145 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2145 of the 2145 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 46: 46: NOTE 3 [file unknown]: 46: You are using constraints on all bonds, whereas the forcefield has been 46: parametrized only with constraints involving hydrogen atoms. We suggest 46: using constraints = h-bonds instead, this will also improve performance. 46: 46: Cleaning up constraints and constant bonded interactions with virtual sites 46: Removed 18 Angles with virtual sites, 21 left 46: Removed 10 Proper Dih.s with virtual sites, 44 left 46: Converted 15 Constraints with virtual sites to connections, 7 left 46: Number of degrees of freedom in T-Coupling group System is 23.00 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 46: NVE simulation: will use the initial temperature of 456.887 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 5 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 46: There are 9 non-linear virtual site constructions. Their contribution to 46: the energy error is approximated. In most cases this does not affect the 46: error significantly. 46: 46: 46: NOTE 6 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 6 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'Alanine dipeptide in vacuo' 46: 16 steps, 0.0 ps. 46: turning all bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 46: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.012 0.006 196.4 46: (ns/day) (hour/ns) 46: Performance: 240.142 0.100 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 14 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.002 0.001 193.9 46: (ns/day) (hour/ns) 46: Performance: 1327.142 0.018 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (89 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2145 of the 2145 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2145 of the 2145 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 46: 46: NOTE 3 [file unknown]: 46: You are using constraints on all bonds, whereas the forcefield has been 46: parametrized only with constraints involving hydrogen atoms. We suggest 46: using constraints = h-bonds instead, this will also improve performance. 46: 46: Cleaning up constraints and constant bonded interactions with virtual sites 46: Removed 18 Angles with virtual sites, 21 left 46: Removed 10 Proper Dih.s with virtual sites, 44 left 46: Converted 15 Constraints with virtual sites to connections, 7 left 46: Number of degrees of freedom in T-Coupling group System is 23.00 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 46: NVE simulation: will use the initial temperature of 456.887 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 5 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 46: There are 9 non-linear virtual site constructions. Their contribution to 46: the energy error is approximated. In most cases this does not affect the 46: error significantly. 46: 46: 46: NOTE 6 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 6 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'Alanine dipeptide in vacuo' 46: 16 steps, 0.0 ps. 46: turning all bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 46: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.173 0.087 199.7 46: (ns/day) (hour/ns) 46: Performance: 16.946 1.416 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 14 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 194.8 46: (ns/day) (hour/ns) 46: Performance: 863.675 0.028 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (132 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2145 of the 2145 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2145 of the 2145 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 46: 46: NOTE 3 [file unknown]: 46: You are using constraints on all bonds, whereas the forcefield has been 46: parametrized only with constraints involving hydrogen atoms. We suggest 46: using constraints = h-bonds instead, this will also improve performance. 46: 46: Cleaning up constraints and constant bonded interactions with virtual sites 46: Removed 18 Angles with virtual sites, 21 left 46: Removed 10 Proper Dih.s with virtual sites, 44 left 46: Converted 15 Constraints with virtual sites to connections, 7 left 46: Number of degrees of freedom in T-Coupling group System is 23.00 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 46: There are 9 non-linear virtual site constructions. Their contribution to 46: the energy error is approximated. In most cases this does not affect the 46: error significantly. 46: 46: 46: NOTE 5 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 5 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 100, rlist from 0.745 to 0.873 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'Alanine dipeptide in vacuo' 46: 16 steps, 0.0 ps. 46: turning all bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.015 0.007 198.3 46: (ns/day) (hour/ns) 46: Performance: 199.559 0.120 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 100, rlist from 0.745 to 0.873 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 14 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 194.2 46: (ns/day) (hour/ns) 46: Performance: 1045.054 0.023 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (86 ms) 46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2145 of the 2145 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2145 of the 2145 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 46: 46: NOTE 3 [file unknown]: 46: You are using constraints on all bonds, whereas the forcefield has been 46: parametrized only with constraints involving hydrogen atoms. We suggest 46: using constraints = h-bonds instead, this will also improve performance. 46: 46: Cleaning up constraints and constant bonded interactions with virtual sites 46: Removed 18 Angles with virtual sites, 21 left 46: Removed 10 Proper Dih.s with virtual sites, 44 left 46: Converted 15 Constraints with virtual sites to connections, 7 left 46: Number of degrees of freedom in T-Coupling group System is 23.00 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 46: There are 9 non-linear virtual site constructions. Their contribution to 46: the energy error is approximated. In most cases this does not affect the 46: error significantly. 46: 46: 46: NOTE 5 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 5 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 40, rlist from 0.727 to 0.874 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'Alanine dipeptide in vacuo' 46: 16 steps, 0.0 ps. 46: turning all bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.098 0.049 199.6 46: (ns/day) (hour/ns) 46: Performance: 30.013 0.800 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 40, rlist from 0.727 to 0.874 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 11 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 191.1 46: (ns/day) (hour/ns) 46: Performance: 955.131 0.025 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (100 ms) 46: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (3300 ms total) 46: 46: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.011 0.006 197.6 46: (ns/day) (hour/ns) 46: Performance: 252.411 0.095 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 11 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 189.1 46: (ns/day) (hour/ns) 46: Performance: 977.717 0.025 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (32 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.014 0.007 196.1 46: (ns/day) (hour/ns) 46: Performance: 201.202 0.119 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 11 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.004 0.002 188.2 46: (ns/day) (hour/ns) 46: Performance: 745.203 0.032 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (79 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.011 0.006 196.7 46: (ns/day) (hour/ns) 46: Performance: 251.782 0.095 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 186.9 46: (ns/day) (hour/ns) 46: Performance: 805.728 0.030 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (75 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.011 0.006 197.0 46: (ns/day) (hour/ns) 46: Performance: 251.977 0.095 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 11 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 183.6 46: (ns/day) (hour/ns) 46: Performance: 992.364 0.024 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (37 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.013 0.006 197.5 46: (ns/day) (hour/ns) 46: Performance: 226.993 0.106 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 10 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.004 0.002 188.3 46: (ns/day) (hour/ns) 46: Performance: 768.729 0.031 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (78 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.011 0.005 197.0 46: (ns/day) (hour/ns) 46: Performance: 268.517 0.089 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 11 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 186.8 46: (ns/day) (hour/ns) 46: Performance: 1072.714 0.022 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (30 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.013 0.007 195.8 46: (ns/day) (hour/ns) 46: Performance: 219.496 0.109 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 12 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.004 0.002 186.9 46: (ns/day) (hour/ns) 46: Performance: 701.343 0.034 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (75 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.013 0.007 196.4 46: (ns/day) (hour/ns) 46: Performance: 221.445 0.108 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 12 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.004 0.002 188.9 46: (ns/day) (hour/ns) 46: Performance: 733.142 0.033 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (83 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.016 0.008 196.3 46: (ns/day) (hour/ns) 46: Performance: 176.547 0.136 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 11 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 186.7 46: (ns/day) (hour/ns) 46: Performance: 827.258 0.029 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (54 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.011 0.006 191.5 46: (ns/day) (hour/ns) 46: Performance: 262.142 0.092 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 12 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.004 0.002 189.6 46: (ns/day) (hour/ns) 46: Performance: 632.894 0.038 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (76 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.086 0.043 199.3 46: (ns/day) (hour/ns) 46: Performance: 34.094 0.704 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 11 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.004 0.002 188.1 46: (ns/day) (hour/ns) 46: Performance: 755.067 0.032 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (74 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.014 0.007 198.7 46: (ns/day) (hour/ns) 46: Performance: 215.594 0.111 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 10 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.004 0.002 188.3 46: (ns/day) (hour/ns) 46: Performance: 771.231 0.031 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (87 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.015 0.008 198.9 46: (ns/day) (hour/ns) 46: Performance: 195.178 0.123 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 12 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 186.0 46: (ns/day) (hour/ns) 46: Performance: 1043.461 0.023 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (49 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.015 0.007 198.6 46: (ns/day) (hour/ns) 46: Performance: 199.243 0.120 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 188.9 46: (ns/day) (hour/ns) 46: Performance: 847.050 0.028 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (75 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.011 0.005 198.7 46: (ns/day) (hour/ns) 46: Performance: 267.167 0.090 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 12 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 187.7 46: (ns/day) (hour/ns) 46: Performance: 942.563 0.025 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (73 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.015 0.007 198.8 46: (ns/day) (hour/ns) 46: Performance: 198.026 0.121 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 10 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.004 0.002 188.3 46: (ns/day) (hour/ns) 46: Performance: 695.719 0.034 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (51 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.013 0.006 199.0 46: (ns/day) (hour/ns) 46: Performance: 231.810 0.104 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 12 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 187.9 46: (ns/day) (hour/ns) 46: Performance: 1074.397 0.022 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (71 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.011 0.006 198.4 46: (ns/day) (hour/ns) 46: Performance: 260.402 0.092 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 11 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 186.3 46: (ns/day) (hour/ns) 46: Performance: 906.370 0.026 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (33 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.014 0.007 198.5 46: (ns/day) (hour/ns) 46: Performance: 206.413 0.116 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 12 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.004 0.002 188.6 46: (ns/day) (hour/ns) 46: Performance: 721.043 0.033 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (78 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.102 0.051 199.8 46: (ns/day) (hour/ns) 46: Performance: 28.826 0.833 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 11 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 183.4 46: (ns/day) (hour/ns) 46: Performance: 1040.817 0.023 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (82 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.013 0.006 198.6 46: (ns/day) (hour/ns) 46: Performance: 232.897 0.103 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 13 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.004 0.002 187.4 46: (ns/day) (hour/ns) 46: Performance: 685.959 0.035 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (37 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 46: NVE simulation: will use the initial temperature of 293.480 K for 46: determining the Verlet buffer size 46: 46: 46: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 4 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.015 0.007 198.5 46: (ns/day) (hour/ns) 46: Performance: 199.018 0.121 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 12 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 184.5 46: (ns/day) (hour/ns) 46: Performance: 1011.260 0.024 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (84 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.015 0.008 196.2 46: (ns/day) (hour/ns) 46: Performance: 192.886 0.124 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 11 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 185.9 46: (ns/day) (hour/ns) 46: Performance: 1025.740 0.023 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (93 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.023 0.011 196.8 46: (ns/day) (hour/ns) 46: Performance: 128.335 0.187 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 12 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 186.2 46: (ns/day) (hour/ns) 46: Performance: 857.663 0.028 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (116 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.021 0.011 196.7 46: (ns/day) (hour/ns) 46: Performance: 138.167 0.174 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 11 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.004 0.002 188.9 46: (ns/day) (hour/ns) 46: Performance: 665.004 0.036 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (159 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.012 0.006 196.5 46: (ns/day) (hour/ns) 46: Performance: 233.745 0.103 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 11 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 188.0 46: (ns/day) (hour/ns) 46: Performance: 973.853 0.025 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (56 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.013 0.007 197.0 46: (ns/day) (hour/ns) 46: Performance: 215.549 0.111 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 14 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.004 0.002 187.1 46: (ns/day) (hour/ns) 46: Performance: 759.255 0.032 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (98 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.013 0.007 196.2 46: (ns/day) (hour/ns) 46: Performance: 221.461 0.108 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.004 0.002 187.4 46: (ns/day) (hour/ns) 46: Performance: 689.722 0.035 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (97 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.014 0.007 196.8 46: (ns/day) (hour/ns) 46: Performance: 210.238 0.114 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 12 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 183.9 46: (ns/day) (hour/ns) 46: Performance: 952.915 0.025 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (100 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.011 0.006 196.6 46: (ns/day) (hour/ns) 46: Performance: 264.007 0.091 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 16 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 187.5 46: (ns/day) (hour/ns) 46: Performance: 920.728 0.026 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (91 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.020 0.010 196.6 46: (ns/day) (hour/ns) 46: Performance: 144.683 0.166 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 11 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.002 186.2 46: (ns/day) (hour/ns) 46: Performance: 859.098 0.028 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (97 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.015 0.008 196.0 46: (ns/day) (hour/ns) 46: Performance: 188.311 0.127 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.004 0.002 187.7 46: (ns/day) (hour/ns) 46: Performance: 711.960 0.034 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (90 ms) 46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: 46: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (4) 46: 46: Generated 2485 of the 2485 non-bonded parameter combinations 46: Generating 1-4 interactions: fudge = 0.5 46: Generated 2485 of the 2485 1-4 parameter combinations 46: Excluding 3 bonded neighbours molecule type 'nonanol' 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: Number of degrees of freedom in T-Coupling group System is 79.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun '30 system in water' 46: 16 steps, 0.0 ps. 46: turning H bonds into constraints... 46: turning H bonds into constraints... 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.015 0.008 195.4 46: (ns/day) (hour/ns) 46: Performance: 192.296 0.125 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 46: 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr' 46: 46: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 46: 46: NOTE: 11 % of the run time was spent in pair search, 46: you might want to increase nstlist (this has no effect on accuracy) 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.003 0.001 184.7 46: (ns/day) (hour/ns) 46: Performance: 1010.430 0.024 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as double precision energy file 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 46: 46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (97 ms) 46: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (2509 ms total) 46: 46: [----------] 2 tests from Angles1/SimpleMdrunTest 46: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/0 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: Generated 3 of the 3 non-bonded parameter combinations 46: Excluding 3 bonded neighbours molecule type 'butane' 46: 46: NOTE 2 [file angles1.top, line 72]: 46: In moleculetype 'butane' 4 atoms are not bound by a potential or 46: constraint to any other atom in the same moleculetype. Although 46: technically this might not cause issues in a simulation, this often means 46: that the user forgot to add a bond/potential/constraint or put multiple 46: molecules in the same moleculetype definition by mistake. Run with -v to 46: get information for each atom. 46: 46: Number of degrees of freedom in T-Coupling group System is 9.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]: 46: NVE simulation: will use the initial temperature of 238.919 K for 46: determining the Verlet buffer size 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'This_incredible_box_of_butane' 46: 50 steps, 0.1 ps. 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K 46: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.008 0.004 197.8 46: (ns/day) (hour/ns) 46: Performance: 1061.744 0.023 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 5 time 0.020 Reading energy frame 6 time 0.024 Reading energy frame 7 time 0.028 Reading energy frame 8 time 0.032 Reading energy frame 9 time 0.036 Reading energy frame 10 time 0.040 Reading energy frame 11 time 0.044 Reading energy frame 12 time 0.048 Reading energy frame 13 time 0.050 Last energy frame read 13 time 0.050 46: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/0 (11 ms) 46: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/1 46: 46: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]: 46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 46: that with the Verlet scheme, nstlist has no effect on the accuracy of 46: your simulation. 46: 46: Generated 3 of the 3 non-bonded parameter combinations 46: Excluding 3 bonded neighbours molecule type 'butane' 46: 46: NOTE 2 [file angles1.top, line 72]: 46: In moleculetype 'butane' 4 atoms are not bound by a potential or 46: constraint to any other atom in the same moleculetype. Although 46: technically this might not cause issues in a simulation, this often means 46: that the user forgot to add a bond/potential/constraint or put multiple 46: molecules in the same moleculetype definition by mistake. Run with -v to 46: get information for each atom. 46: 46: Number of degrees of freedom in T-Coupling group System is 9.00 46: 46: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]: 46: NVE simulation: will use the initial temperature of 238.919 K for 46: determining the Verlet buffer size 46: 46: 46: There were 3 notes 46: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 46: log). 46: The current CPU can measure timings more accurately than the code in 46: mdrun-non-integrator-test was configured to use. This might affect your simulation 46: speed as accurate timings are needed for load-balancing. 46: Please consider rebuilding mdrun-non-integrator-test with the GMX_USE_RDTSCP=ON CMake option. 46: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 46: Can not increase nstlist because an NVE ensemble is used 46: 46: Using 1 MPI thread 46: 46: Non-default thread affinity set, disabling internal thread affinity 46: 46: Using 2 OpenMP threads 46: 46: starting mdrun 'This_incredible_box_of_butane' 46: 50 steps, 0.1 ps. 46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K 46: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm 46: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: This run will generate roughly 0 Mb of data 46: 46: Writing final coordinates. 46: 46: Core t (s) Wall t (s) (%) 46: Time: 0.011 0.006 198.7 46: (ns/day) (hour/ns) 46: Performance: 798.763 0.030 46: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.edr as double precision energy file 46: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 5 time 0.020 Reading energy frame 6 time 0.024 Reading energy frame 7 time 0.028 Reading energy frame 8 time 0.032 Reading energy frame 9 time 0.036 Reading energy frame 10 time 0.040 Reading energy frame 11 time 0.044 Reading energy frame 12 time 0.048 Reading energy frame 13 time 0.050 Last energy frame read 13 time 0.050 46: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/1 (58 ms) 46: [----------] 2 tests from Angles1/SimpleMdrunTest (70 ms total) 46: 46: [----------] Global test environment tear-down 46: [==========] 65 tests from 7 test cases ran. (14987 ms total) 46: [ PASSED ] 65 tests. 46/54 Test #46: MdrunNonIntegratorTests ............. Passed 15.07 sec test 47 Start 47: MdrunTpiTests 47: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/mdrun-tpi-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/MdrunTpiTests.xml" 47: Test timeout computed to be: 600 47: [==========] Running 2 tests from 1 test case. 47: [----------] Global test environment set-up. 47: [----------] 2 tests from Simple/TpiTest 47: [ RUN ] Simple/TpiTest.ReproducesOutput/0 47: Ignoring obsolete mdp entry 'ns_type' 47: Generated 331705 of the 331705 non-bonded parameter combinations 47: Generating 1-4 interactions: fudge = 0.5 47: Generated 331705 of the 331705 1-4 parameter combinations 47: Excluding 2 bonded neighbours molecule type 'SOL' 47: Excluding 3 bonded neighbours molecule type 'methane' 47: Number of degrees of freedom in T-Coupling group System is 1308.00 47: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 47: log). 47: The current CPU can measure timings more accurately than the code in 47: mdrun-tpi-test was configured to use. This might affect your simulation 47: speed as accurate timings are needed for load-balancing. 47: Please consider rebuilding mdrun-tpi-test with the GMX_USE_RDTSCP=ON CMake option. 47: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 47: 47: TPI is not implemented for GPUs. 47: 47: Using 1 MPI thread 47: 47: Non-default thread affinity set, disabling internal thread affinity 47: 47: Using 1 OpenMP thread 47: 47: Reading frames from gro file '216 water molecules', 648 atoms. 47: Reading frame 0 time 0.000 mu 8.706e+02 8.706e+02 47: Last frame 0 time 0.000 47: Analysing residue names: 47: There are: 216 Water residues 47: There are: 1 Other residues 47: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 47: This run will generate roughly 0 Mb of data 47: [ OK ] Simple/TpiTest.ReproducesOutput/0 (716 ms) 47: [ RUN ] Simple/TpiTest.ReproducesOutput/1 47: Ignoring obsolete mdp entry 'ns_type' 47: Generated 331705 of the 331705 non-bonded parameter combinations 47: Generating 1-4 interactions: fudge = 0.5 47: Generated 331705 of the 331705 1-4 parameter combinations 47: Excluding 2 bonded neighbours molecule type 'SOL' 47: Excluding 3 bonded neighbours molecule type 'methane' 47: Number of degrees of freedom in T-Coupling group System is 1308.00 47: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 47: log). 47: The current CPU can measure timings more accurately than the code in 47: mdrun-tpi-test was configured to use. This might affect your simulation 47: speed as accurate timings are needed for load-balancing. 47: Please consider rebuilding mdrun-tpi-test with the GMX_USE_RDTSCP=ON CMake option. 47: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 47: 47: TPI is not implemented for GPUs. 47: 47: Using 1 MPI thread 47: 47: Non-default thread affinity set, disabling internal thread affinity 47: 47: Using 1 OpenMP thread 47: 47: Reading frames from gro file '216 water molecules', 648 atoms. 47: Reading frame 0 time 0.000 mu 9.144e+01 9.144e+01 47: Last frame 0 time 0.000 47: Analysing residue names: 47: There are: 216 Water residues 47: There are: 1 Other residues 47: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 47: This run will generate roughly 0 Mb of data 47: [ OK ] Simple/TpiTest.ReproducesOutput/1 (598 ms) 47: [----------] 2 tests from Simple/TpiTest (1314 ms total) 47: 47: [----------] Global test environment tear-down 47: [==========] 2 tests from 1 test case ran. (1314 ms total) 47: [ PASSED ] 2 tests. 47/54 Test #47: MdrunTpiTests ....................... Passed 1.33 sec test 48 Start 48: MdrunMpiTests 48: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/MdrunMpiTests.xml" 48: Test timeout computed to be: 600 48: [==========] Running 22 tests from 7 test cases. 48: [----------] Global test environment set-up. 48: [----------] 1 test from DomainDecompositionSpecialCasesTest 48: [ RUN ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: 48: For a correct single-point energy evaluation with nsteps = 0, use 48: continuation = yes to avoid constraining the input coordinates. 48: 48: Setting the LD random seed to -4194313 48: Generated 3 of the 3 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 0.5 48: Generated 3 of the 3 1-4 parameter combinations 48: Excluding 2 bonded neighbours molecule type 'SOL' 48: Number of degrees of freedom in T-Coupling group rest is 9.00 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: 48: NVE simulation with an initial temperature of zero: will use a Verlet 48: buffer of 10%. Check your energy drift! 48: 48: 48: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting mdrun 'spc2' 48: 0 steps, 0.0 ps. 48: 48: NOTE: 16 % of the run time was spent in domain decomposition, 48: 14 % of the run time was spent in pair search, 48: you might want to increase nstlist (this has no effect on accuracy) 48: 48: Core t (s) Wall t (s) (%) 48: Time: 0.001 0.000 259.2 48: (ns/day) (hour/ns) 48: Performance: 227.416 0.106 48: This run will generate roughly 0 Mb of data 48: [ OK ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks (52 ms) 48: [----------] 1 test from DomainDecompositionSpecialCasesTest (52 ms total) 48: 48: [----------] 4 tests from MimicTest 48: [ RUN ] MimicTest.OneQuantumMol 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 48: For a correct single-point energy evaluation with nsteps = 0, use 48: continuation = yes to avoid constraining the input coordinates. 48: 48: Setting the LD random seed to -672154147 48: Generated 10 of the 10 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 0.5 48: Generated 10 of the 10 1-4 parameter combinations 48: Excluding 2 bonded neighbours molecule type 'SOL' 48: Number of degrees of freedom in T-Coupling group rest is 21.00 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 48: NVE simulation with an initial temperature of zero: will use a Verlet 48: buffer of 10%. Check your energy drift! 48: 48: 48: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/4water.gro' 48: 48: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: 48: NOTE: 18 % of the run time was spent in domain decomposition, 48: 11 % of the run time was spent in pair search, 48: you might want to increase nstlist (this has no effect on accuracy) 48: 48: Core t (s) Wall t (s) (%) 48: Time: 0.001 0.000 378.8 48: (ns/day) (hour/ns) 48: Performance: 290.724 0.083 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 48: [ OK ] MimicTest.OneQuantumMol (5 ms) 48: [ RUN ] MimicTest.AllQuantumMol 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 48: For a correct single-point energy evaluation with nsteps = 0, use 48: continuation = yes to avoid constraining the input coordinates. 48: 48: Setting the LD random seed to -34652211 48: Generated 10 of the 10 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 0.5 48: Generated 10 of the 10 1-4 parameter combinations 48: Excluding 2 bonded neighbours molecule type 'SOL' 48: Number of degrees of freedom in T-Coupling group rest is 21.00 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 48: NVE simulation with an initial temperature of zero: will use a Verlet 48: buffer of 10%. Check your energy drift! 48: 48: 48: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/4water.gro' 48: 48: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: 48: NOTE: 18 % of the run time was spent in domain decomposition, 48: 12 % of the run time was spent in pair search, 48: you might want to increase nstlist (this has no effect on accuracy) 48: 48: Core t (s) Wall t (s) (%) 48: Time: 0.001 0.000 379.5 48: (ns/day) (hour/ns) 48: Performance: 281.466 0.085 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 48: [ OK ] MimicTest.AllQuantumMol (6 ms) 48: [ RUN ] MimicTest.TwoQuantumMol 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 48: For a correct single-point energy evaluation with nsteps = 0, use 48: continuation = yes to avoid constraining the input coordinates. 48: 48: Setting the LD random seed to -151126597 48: Generated 10 of the 10 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 0.5 48: Generated 10 of the 10 1-4 parameter combinations 48: Excluding 2 bonded neighbours molecule type 'SOL' 48: Number of degrees of freedom in T-Coupling group rest is 21.00 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 48: NVE simulation with an initial temperature of zero: will use a Verlet 48: buffer of 10%. Check your energy drift! 48: 48: 48: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/4water.gro' 48: 48: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: 48: NOTE: 17 % of the run time was spent in domain decomposition, 48: 14 % of the run time was spent in pair search, 48: you might want to increase nstlist (this has no effect on accuracy) 48: 48: Core t (s) Wall t (s) (%) 48: Time: 0.003 0.001 382.8 48: (ns/day) (hour/ns) 48: Performance: 127.042 0.189 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 48: [ OK ] MimicTest.TwoQuantumMol (42 ms) 48: [ RUN ] MimicTest.BondCuts 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 48: For a correct single-point energy evaluation with nsteps = 0, use 48: continuation = yes to avoid constraining the input coordinates. 48: 48: Setting the LD random seed to -599890761 48: Generated 2211 of the 2211 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 0.5 48: Generated 2211 of the 2211 1-4 parameter combinations 48: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 48: Number of degrees of freedom in T-Coupling group rest is 66.00 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 48: NVE simulation: will use the initial temperature of 300.368 K for 48: determining the Verlet buffer size 48: 48: 48: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/gromacs-5atmZb/gromacs-2020.6/src/testutils/simulationdatabase/ala.gro' 48: 48: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: 48: NOTE: 12 % of the run time was spent in domain decomposition, 48: 12 % of the run time was spent in pair search, 48: you might want to increase nstlist (this has no effect on accuracy) 48: 48: Core t (s) Wall t (s) (%) 48: Time: 0.003 0.001 386.4 48: (ns/day) (hour/ns) 48: Performance: 128.075 0.187 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 48: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm 48: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm 48: Note that mdrun will redetermine rlist based on the actual pair-list setup 48: This run will generate roughly 0 Mb of data 48: [ OK ] MimicTest.BondCuts (26 ms) 48: [----------] 4 tests from MimicTest (79 ms total) 48: 48: [----------] 1 test from MultiSimTerminationTest 48: [ RUN ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 48: [ OK ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms) 48: [----------] 1 test from MultiSimTerminationTest (0 ms total) 48: 48: [----------] 3 tests from PmeTest 48: [ RUN ] PmeTest.ReproducesEnergies 48: Setting the LD random seed to 2147482206 48: Generated 8 of the 10 non-bonded parameter combinations 48: Excluding 2 bonded neighbours molecule type 'Methanol' 48: Excluding 2 bonded neighbours molecule type 'SOL' 48: Number of degrees of freedom in T-Coupling group rest is 12.00 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]: 48: NVE simulation: will use the initial temperature of 1046.791 K for 48: determining the Verlet buffer size 48: 48: Estimate for the relative computational load of the PME mesh part: 1.00 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]: 48: The optimal PME mesh load for parallel simulations is below 0.5 48: and for highly parallel simulations between 0.25 and 0.33, 48: for higher performance, increase the cut-off and the PME grid spacing. 48: 48: 48: 48: There were 2 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: Using 0 OpenMP thread per tMPI thread for PME 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting mdrun 'spc-and-methanol' 48: 20 steps, 0.0 ps. 48: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 48: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 48: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 48: Note that mdrun will redetermine rlist based on the actual pair-list setup 48: Calculating fourier grid dimensions for X Y Z 48: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 48: This run will generate roughly 0 Mb of data 48: 48: Writing final coordinates. 48: 48: Core t (s) Wall t (s) (%) 48: Time: 0.378 0.095 399.7 48: (ns/day) (hour/ns) 48: Performance: 19.194 1.250 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: Using 0 OpenMP thread per tMPI thread for PME 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting mdrun 'spc-and-methanol' 48: 20 steps, 0.0 ps. 48: 48: Writing final coordinates. 48: 48: Core t (s) Wall t (s) (%) 48: Time: 0.408 0.102 399.7 48: (ns/day) (hour/ns) 48: Performance: 17.756 1.352 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: Using 0 OpenMP thread per tMPI thread for PME 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting mdrun 'spc-and-methanol' 48: 20 steps, 0.0 ps. 48: 48: Writing final coordinates. 48: 48: Core t (s) Wall t (s) (%) 48: Time: 0.400 0.100 399.7 48: (ns/day) (hour/ns) 48: Performance: 18.122 1.324 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (782 ms) 48: [ RUN ] PmeTest.ScalesTheBox 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 48: For a correct single-point energy evaluation with nsteps = 0, use 48: continuation = yes to avoid constraining the input coordinates. 48: 48: Setting the LD random seed to -1224774658 48: Generated 8 of the 10 non-bonded parameter combinations 48: Excluding 2 bonded neighbours molecule type 'Methanol' 48: Excluding 2 bonded neighbours molecule type 'SOL' 48: Number of degrees of freedom in T-Coupling group rest is 12.00 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 48: NVE simulation: will use the initial temperature of 1046.791 K for 48: determining the Verlet buffer size 48: 48: Estimate for the relative computational load of the PME mesh part: 1.00 48: 48: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 48: The optimal PME mesh load for parallel simulations is below 0.5 48: and for highly parallel simulations between 0.25 and 0.33, 48: for higher performance, increase the cut-off and the PME grid spacing. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: Using 0 OpenMP thread per tMPI thread for PME 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting mdrun 'spc-and-methanol' 48: 0 steps, 0.0 ps. 48: 48: Core t (s) Wall t (s) (%) 48: Time: 0.004 0.001 364.1 48: (ns/day) (hour/ns) 48: Performance: 84.178 0.285 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 48: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 48: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 48: Note that mdrun will redetermine rlist based on the actual pair-list setup 48: Calculating fourier grid dimensions for X Y Z 48: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 48: This run will generate roughly 0 Mb of data 48: [ OK ] PmeTest.ScalesTheBox (99 ms) 48: [ RUN ] PmeTest.ScalesTheBoxWithWalls 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]: 48: For a correct single-point energy evaluation with nsteps = 0, use 48: continuation = yes to avoid constraining the input coordinates. 48: 48: Setting the LD random seed to -17533313 48: Generated 8 of the 10 non-bonded parameter combinations 48: Excluding 2 bonded neighbours molecule type 'Methanol' 48: Excluding 2 bonded neighbours molecule type 'SOL' 48: Searching the wall atom type(s) 48: Number of degrees of freedom in T-Coupling group rest is 13.00 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]: 48: NVE simulation: will use the initial temperature of 966.268 K for 48: determining the Verlet buffer size 48: 48: Estimate for the relative computational load of the PME mesh part: 1.00 48: 48: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]: 48: The optimal PME mesh load for parallel simulations is below 0.5 48: and for highly parallel simulations between 0.25 and 0.33, 48: for higher performance, increase the cut-off and the PME grid spacing. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: Can not increase nstlist because an NVE ensemble is used 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: Using 0 OpenMP thread per tMPI thread for PME 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: starting mdrun 'spc-and-methanol' 48: 0 steps, 0.0 ps. 48: 48: Core t (s) Wall t (s) (%) 48: Time: 0.267 0.067 399.3 48: (ns/day) (hour/ns) 48: Performance: 1.295 18.539 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 48: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 48: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 48: Note that mdrun will redetermine rlist based on the actual pair-list setup 48: Calculating fourier grid dimensions for X Y Z 48: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118 48: This run will generate roughly 0 Mb of data 48: [ OK ] PmeTest.ScalesTheBoxWithWalls (1487 ms) 48: [----------] 3 tests from PmeTest (2369 ms total) 48: 48: [----------] 1 test from ReplicaExchangeTerminationTest 48: [ RUN ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 48: [ OK ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms) 48: [----------] 1 test from ReplicaExchangeTerminationTest (0 ms total) 48: 48: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 330891 of the 330891 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 0.5 48: Generated 330891 of the 330891 1-4 parameter combinations 48: Excluding 2 bonded neighbours molecule type 'SOL' 48: Number of degrees of freedom in T-Coupling group System is 27.00 48: 48: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Steepest Descents: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: 48: Energy minimization reached the maximum number of steps before the forces 48: reached the requested precision Fmax < 10. 48: 48: writing lowest energy coordinates. 48: 48: Steepest Descents did not converge to Fmax < 10 in 5 steps. 48: Potential Energy = -4.79910463671046e+01 48: Maximum force = 1.86297359432217e+02 on atom 13 48: Norm of force = 8.77219865482096e+01 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (808 ms) 48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 330891 of the 330891 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 0.5 48: Generated 330891 of the 330891 1-4 parameter combinations 48: Excluding 2 bonded neighbours molecule type 'SOL' 48: Number of degrees of freedom in T-Coupling group System is 27.00 48: 48: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Polak-Ribiere Conjugate Gradients: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: F-max = 3.02331e+02 on atom 3 48: F-Norm = 1.18024e+02 48: 48: 48: Energy minimization reached the maximum number of steps before the forces 48: reached the requested precision Fmax < 10. 48: 48: writing lowest energy coordinates. 48: 48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 48: Potential Energy = -5.58622538633254e+01 48: Maximum force = 4.27274822366625e+02 on atom 13 48: Norm of force = 1.84530029253875e+02 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (643 ms) 48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 20503 of the 20503 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 1 48: Generated 17396 of the 20503 1-4 parameter combinations 48: Excluding 3 bonded neighbours molecule type 'Glycine' 48: Number of degrees of freedom in T-Coupling group System is 22.00 48: 48: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Steepest Descents: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: 48: Energy minimization reached the maximum number of steps before the forces 48: reached the requested precision Fmax < 10. 48: 48: writing lowest energy coordinates. 48: 48: Steepest Descents did not converge to Fmax < 10 in 5 steps. 48: Potential Energy = 3.19376899751522e+02 48: Maximum force = 9.99884921009767e+03 on atom 9 48: Norm of force = 4.61669565054298e+03 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 turning H bonds into constraints... 48: This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (247 ms) 48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 20503 of the 20503 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 1 48: Generated 17396 of the 20503 1-4 parameter combinations 48: Excluding 3 bonded neighbours molecule type 'Glycine' 48: 48: NOTE 3 [file glycine_vacuo.top, line 12]: 48: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 48: 48: Number of degrees of freedom in T-Coupling group System is 22.00 48: 48: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 4 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Polak-Ribiere Conjugate Gradients: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: F-max = 2.41575e+04 on atom 10 48: F-Norm = 1.18451e+04 48: 48: 48: Energy minimization reached the maximum number of steps before the forces 48: reached the requested precision Fmax < 10. 48: 48: writing lowest energy coordinates. 48: 48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 48: Potential Energy = 1.51743018140930e+02 48: Maximum force = 7.42089573409109e+03 on atom 9 48: Norm of force = 3.56929298615740e+03 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 turning H bonds into constraints... 48: This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (244 ms) 48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 2145 of the 2145 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 0.5 48: Generated 2145 of the 2145 1-4 parameter combinations 48: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 48: 48: NOTE 3 [file unknown]: 48: You are using constraints on all bonds, whereas the forcefield has been 48: parametrized only with constraints involving hydrogen atoms. We suggest 48: using constraints = h-bonds instead, this will also improve performance. 48: 48: Cleaning up constraints and constant bonded interactions with virtual sites 48: Removed 18 Angles with virtual sites, 21 left 48: Removed 10 Proper Dih.s with virtual sites, 44 left 48: Converted 15 Constraints with virtual sites to connections, 7 left 48: Number of degrees of freedom in T-Coupling group System is 23.00 48: 48: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 4 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Steepest Descents: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: 48: Energy minimization reached the maximum number of steps before the forces 48: reached the requested precision Fmax < 10. 48: 48: writing lowest energy coordinates. 48: 48: Steepest Descents did not converge to Fmax < 10 in 5 steps. 48: Potential Energy = -1.56984193848274e+02 48: Maximum force = 4.56923624626205e+02 on atom 17 48: Norm of force = 1.83258377168315e+02 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 turning all bonds into constraints... 48: This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (65 ms) 48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 2145 of the 2145 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 0.5 48: Generated 2145 of the 2145 1-4 parameter combinations 48: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 48: 48: NOTE 3 [file unknown]: 48: You are using constraints on all bonds, whereas the forcefield has been 48: parametrized only with constraints involving hydrogen atoms. We suggest 48: using constraints = h-bonds instead, this will also improve performance. 48: 48: 48: NOTE 4 [file unknown]: 48: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 48: 48: Cleaning up constraints and constant bonded interactions with virtual sites 48: Removed 18 Angles with virtual sites, 21 left 48: Removed 10 Proper Dih.s with virtual sites, 44 left 48: Converted 15 Constraints with virtual sites to connections, 7 left 48: Number of degrees of freedom in T-Coupling group System is 23.00 48: 48: NOTE 5 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 5 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Polak-Ribiere Conjugate Gradients: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: F-max = 1.06800e+03 on atom 28 48: F-Norm = 4.26922e+02 48: 48: 48: Energy minimization reached the maximum number of steps before the forces 48: reached the requested precision Fmax < 10. 48: 48: writing lowest energy coordinates. 48: 48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 48: Potential Energy = -1.69410778678182e+02 48: Maximum force = 2.18225948474131e+02 on atom 17 48: Norm of force = 7.92068036537818e+01 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 turning all bonds into constraints... 48: This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (21 ms) 48: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (2028 ms total) 48: 48: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 1 of the 1 non-bonded parameter combinations 48: Excluding 1 bonded neighbours molecule type 'Argon' 48: Number of degrees of freedom in T-Coupling group System is 33.00 48: 48: There were 2 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Steepest Descents: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: 48: writing lowest energy coordinates. 48: 48: Steepest Descents converged to Fmax < 10 in 1 steps 48: Potential Energy = -9.74257075835447e-01 48: Maximum force = 4.01322929015133e+00 on atom 3 48: Norm of force = 1.63839399694378e+00 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (73 ms) 48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 1 of the 1 non-bonded parameter combinations 48: Excluding 1 bonded neighbours molecule type 'Argon' 48: Number of degrees of freedom in T-Coupling group System is 33.00 48: 48: There were 2 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Polak-Ribiere Conjugate Gradients: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: F-max = 4.01323e+00 on atom 3 48: F-Norm = 1.63839e+00 48: 48: 48: writing lowest energy coordinates. 48: 48: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 48: Potential Energy = -9.90642313893957e-01 48: Maximum force = 2.57812909491105e+00 on atom 3 48: Norm of force = 1.05251679559258e+00 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (14 ms) 48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: 48: WARNING 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 48: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 48: 48: Generated 1 of the 1 non-bonded parameter combinations 48: Excluding 1 bonded neighbours molecule type 'Argon' 48: Number of degrees of freedom in T-Coupling group System is 33.00 48: 48: There were 2 notes 48: 48: There was 1 warning 48: This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (26 ms) 48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 20503 of the 20503 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 1 48: Generated 17396 of the 20503 1-4 parameter combinations 48: Excluding 3 bonded neighbours molecule type 'Glycine' 48: Number of degrees of freedom in T-Coupling group System is 27.00 48: 48: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Steepest Descents: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: 48: Energy minimization reached the maximum number of steps before the forces 48: reached the requested precision Fmax < 10. 48: 48: writing lowest energy coordinates. 48: 48: Steepest Descents did not converge to Fmax < 10 in 5 steps. 48: Potential Energy = 3.19395484891520e+02 48: Maximum force = 9.97041707197911e+03 on atom 9 48: Norm of force = 4.62274878665467e+03 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (192 ms) 48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: Generated 20503 of the 20503 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 1 48: Generated 17396 of the 20503 1-4 parameter combinations 48: Excluding 3 bonded neighbours molecule type 'Glycine' 48: Number of degrees of freedom in T-Coupling group System is 27.00 48: 48: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 48: log). 48: The current CPU can measure timings more accurately than the code in 48: mdrun-mpi-test was configured to use. This might affect your simulation 48: speed as accurate timings are needed for load-balancing. 48: Please consider rebuilding mdrun-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 48: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 48: 48: Using 2 MPI threads 48: Using 2 OpenMP threads per tMPI thread 48: 48: 48: NOTE: The number of threads is not equal to the number of (logical) cores 48: and the -pin option is set to auto: will not pin threads to cores. 48: This can lead to significant performance degradation. 48: Consider using -pin on (and -pinoffset in case you run multiple jobs). 48: 48: Polak-Ribiere Conjugate Gradients: 48: Tolerance (Fmax) = 1.00000e+01 48: Number of steps = 4 48: F-max = 2.41672e+04 on atom 10 48: F-Norm = 1.19357e+04 48: 48: 48: Energy minimization reached the maximum number of steps before the forces 48: reached the requested precision Fmax < 10. 48: 48: writing lowest energy coordinates. 48: 48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 48: Potential Energy = 1.56258793899481e+02 48: Maximum force = 7.50181017480396e+03 on atom 9 48: Norm of force = 3.61390332564874e+03 48: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 48: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (231 ms) 48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 48: 48: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 48: that with the Verlet scheme, nstlist has no effect on the accuracy of 48: your simulation. 48: 48: 48: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting 48: nstcomm to nstcalcenergy 48: 48: 48: WARNING 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 48: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 48: 48: Generated 20503 of the 20503 non-bonded parameter combinations 48: Generating 1-4 interactions: fudge = 1 48: Generated 17396 of the 20503 1-4 parameter combinations 48: Excluding 3 bonded neighbours molecule type 'Glycine' 48: Number of degrees of freedom in T-Coupling group System is 27.00 48: 48: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 48: You are using a plain Coulomb cut-off, which might produce artifacts. 48: You might want to consider using PME electrostatics. 48: 48: 48: 48: There were 3 notes 48: 48: There was 1 warning 48: This run will generate roughly 0 Mb of data 48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (193 ms) 48: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (729 ms total) 48: 48: [----------] Global test environment tear-down 48: [==========] 22 tests from 7 test cases ran. (5257 ms total) 48: [ PASSED ] 22 tests. 48: 48: YOU HAVE 4 DISABLED TESTS 48: 48/54 Test #48: MdrunMpiTests ....................... Passed 5.34 sec test 49 Start 49: MdrunMpiCoordinationTestsOneRank 49: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/mdrun-mpi-coordination-test "-ntmpi" "1" "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/MdrunMpiCoordinationTestsOneRank.xml" 49: Test timeout computed to be: 960 49: [==========] Running 27 tests from 3 test cases. 49: [----------] Global test environment set-up. 49: [----------] 1 test from BasicPropagators/PeriodicActionsTest 49: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 99.2 49: (ns/day) (hour/ns) 49: Performance: 356.702 0.067 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.004 97.9 49: (ns/day) (hour/ns) 49: Performance: 416.256 0.058 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.3 49: (ns/day) (hour/ns) 49: Performance: 519.531 0.046 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.4 49: (ns/day) (hour/ns) 49: Performance: 365.918 0.066 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.004 98.5 49: (ns/day) (hour/ns) 49: Performance: 418.263 0.057 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.004 98.9 49: (ns/day) (hour/ns) 49: Performance: 417.158 0.058 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 49: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (129 ms) 49: [----------] 1 test from BasicPropagators/PeriodicActionsTest (130 ms total) 49: 49: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 99.0 49: (ns/day) (hour/ns) 49: Performance: 431.747 0.056 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.9 49: (ns/day) (hour/ns) 49: Performance: 517.306 0.046 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 99.0 49: (ns/day) (hour/ns) 49: Performance: 492.375 0.049 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.029 0.029 99.7 49: (ns/day) (hour/ns) 49: Performance: 50.578 0.475 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.5 49: (ns/day) (hour/ns) 49: Performance: 340.082 0.071 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.6 49: (ns/day) (hour/ns) 49: Performance: 371.120 0.065 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (81 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.2 49: (ns/day) (hour/ns) 49: Performance: 379.674 0.063 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.0 49: (ns/day) (hour/ns) 49: Performance: 349.636 0.069 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 97.8 49: (ns/day) (hour/ns) 49: Performance: 397.560 0.060 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.2 49: (ns/day) (hour/ns) 49: Performance: 348.963 0.069 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 97.7 49: (ns/day) (hour/ns) 49: Performance: 346.412 0.069 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.0 49: (ns/day) (hour/ns) 49: Performance: 395.798 0.061 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (125 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 97.6 49: (ns/day) (hour/ns) 49: Performance: 491.903 0.049 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.9 49: (ns/day) (hour/ns) 49: Performance: 334.979 0.072 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.006 98.8 49: (ns/day) (hour/ns) 49: Performance: 229.317 0.105 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 97.2 49: (ns/day) (hour/ns) 49: Performance: 439.728 0.055 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.2 49: (ns/day) (hour/ns) 49: Performance: 404.345 0.059 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.1 49: (ns/day) (hour/ns) 49: Performance: 361.877 0.066 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (87 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 97.9 49: (ns/day) (hour/ns) 49: Performance: 474.476 0.051 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 97.3 49: (ns/day) (hour/ns) 49: Performance: 436.117 0.055 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.6 49: (ns/day) (hour/ns) 49: Performance: 467.491 0.051 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.1 49: (ns/day) (hour/ns) 49: Performance: 527.764 0.045 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.018 0.018 99.5 49: (ns/day) (hour/ns) 49: Performance: 79.681 0.301 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 98.6 49: (ns/day) (hour/ns) 49: Performance: 319.235 0.075 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (76 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 96.8 49: (ns/day) (hour/ns) 49: Performance: 500.658 0.048 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 97.5 49: (ns/day) (hour/ns) 49: Performance: 468.986 0.051 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.0 49: (ns/day) (hour/ns) 49: Performance: 378.717 0.063 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.0 49: (ns/day) (hour/ns) 49: Performance: 386.293 0.062 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.2 49: (ns/day) (hour/ns) 49: Performance: 446.485 0.054 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.004 98.6 49: (ns/day) (hour/ns) 49: Performance: 418.490 0.057 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (59 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 98.1 49: (ns/day) (hour/ns) 49: Performance: 292.776 0.082 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 97.3 49: (ns/day) (hour/ns) 49: Performance: 458.139 0.052 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 97.9 49: (ns/day) (hour/ns) 49: Performance: 621.341 0.039 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.1 49: (ns/day) (hour/ns) 49: Performance: 549.562 0.044 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 96.9 49: (ns/day) (hour/ns) 49: Performance: 432.231 0.056 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 97.3 49: (ns/day) (hour/ns) 49: Performance: 426.486 0.056 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (65 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 97.8 49: (ns/day) (hour/ns) 49: Performance: 565.088 0.042 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.002 0.002 98.4 49: (ns/day) (hour/ns) 49: Performance: 635.047 0.038 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.9 49: (ns/day) (hour/ns) 49: Performance: 493.994 0.049 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 99.0 49: (ns/day) (hour/ns) 49: Performance: 460.950 0.052 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 99.0 49: (ns/day) (hour/ns) 49: Performance: 486.311 0.049 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.017 0.018 99.7 49: (ns/day) (hour/ns) 49: Performance: 83.914 0.286 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (62 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: 49: WARNING 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Using Berendsen pressure coupling invalidates the true ensemble for the 49: thermostat 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: 49: There was 1 warning 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.005 98.5 49: (ns/day) (hour/ns) 49: Performance: 325.183 0.074 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: 49: WARNING 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Using Berendsen pressure coupling invalidates the true ensemble for the 49: thermostat 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: 49: There was 1 warning 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.5 49: (ns/day) (hour/ns) 49: Performance: 524.395 0.046 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: 49: WARNING 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Using Berendsen pressure coupling invalidates the true ensemble for the 49: thermostat 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: 49: There was 1 warning 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 97.9 49: (ns/day) (hour/ns) 49: Performance: 449.154 0.053 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: 49: WARNING 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Using Berendsen pressure coupling invalidates the true ensemble for the 49: thermostat 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: 49: There was 1 warning 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.2 49: (ns/day) (hour/ns) 49: Performance: 387.654 0.062 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: 49: WARNING 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Using Berendsen pressure coupling invalidates the true ensemble for the 49: thermostat 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: 49: There was 1 warning 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.049 0.050 99.8 49: (ns/day) (hour/ns) 49: Performance: 29.650 0.809 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: 49: WARNING 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Using Berendsen pressure coupling invalidates the true ensemble for the 49: thermostat 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: 49: There was 1 warning 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 97.5 49: (ns/day) (hour/ns) 49: Performance: 280.563 0.086 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (116 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.4 49: (ns/day) (hour/ns) 49: Performance: 459.711 0.052 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.5 49: (ns/day) (hour/ns) 49: Performance: 395.189 0.061 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.5 49: (ns/day) (hour/ns) 49: Performance: 397.125 0.060 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.8 49: (ns/day) (hour/ns) 49: Performance: 405.836 0.059 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.8 49: (ns/day) (hour/ns) 49: Performance: 457.017 0.053 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.8 49: (ns/day) (hour/ns) 49: Performance: 433.052 0.055 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (56 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.4 49: (ns/day) (hour/ns) 49: Performance: 501.759 0.048 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.012 0.012 99.2 49: (ns/day) (hour/ns) 49: Performance: 117.940 0.203 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.5 49: (ns/day) (hour/ns) 49: Performance: 423.525 0.057 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.9 49: (ns/day) (hour/ns) 49: Performance: 340.929 0.070 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.004 97.1 49: (ns/day) (hour/ns) 49: Performance: 414.018 0.058 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.005 98.9 49: (ns/day) (hour/ns) 49: Performance: 324.464 0.074 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (73 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 97.4 49: (ns/day) (hour/ns) 49: Performance: 523.059 0.046 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.3 49: (ns/day) (hour/ns) 49: Performance: 480.508 0.050 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.1 49: (ns/day) (hour/ns) 49: Performance: 479.274 0.050 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.006 98.8 49: (ns/day) (hour/ns) 49: Performance: 250.675 0.096 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 98.0 49: (ns/day) (hour/ns) 49: Performance: 288.431 0.083 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.013 0.013 99.2 49: (ns/day) (hour/ns) 49: Performance: 108.995 0.220 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (85 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 97.9 49: (ns/day) (hour/ns) 49: Performance: 388.926 0.062 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.2 49: (ns/day) (hour/ns) 49: Performance: 329.514 0.073 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.045 0.045 99.8 49: (ns/day) (hour/ns) 49: Performance: 32.609 0.736 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.005 98.0 49: (ns/day) (hour/ns) 49: Performance: 320.164 0.075 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 97.9 49: (ns/day) (hour/ns) 49: Performance: 335.599 0.072 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 97.3 49: (ns/day) (hour/ns) 49: Performance: 424.605 0.057 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (111 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 99.0 49: (ns/day) (hour/ns) 49: Performance: 530.537 0.045 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 99.3 49: (ns/day) (hour/ns) 49: Performance: 555.960 0.043 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.039 0.039 99.9 49: (ns/day) (hour/ns) 49: Performance: 38.048 0.631 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.8 49: (ns/day) (hour/ns) 49: Performance: 436.117 0.055 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.8 49: (ns/day) (hour/ns) 49: Performance: 395.645 0.061 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 99.3 49: (ns/day) (hour/ns) 49: Performance: 426.723 0.056 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (90 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 97.9 49: (ns/day) (hour/ns) 49: Performance: 496.502 0.048 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.1 49: (ns/day) (hour/ns) 49: Performance: 369.119 0.065 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.2 49: (ns/day) (hour/ns) 49: Performance: 461.122 0.052 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.1 49: (ns/day) (hour/ns) 49: Performance: 409.559 0.059 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.048 0.048 99.9 49: (ns/day) (hour/ns) 49: Performance: 30.303 0.792 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 49: NVE simulation: will use the initial temperature of 68.810 K for 49: determining the Verlet buffer size 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.041 0.041 99.7 49: (ns/day) (hour/ns) 49: Performance: 36.095 0.665 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (164 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.007 0.007 99.2 49: (ns/day) (hour/ns) 49: Performance: 198.697 0.121 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.009 0.009 99.5 49: (ns/day) (hour/ns) 49: Performance: 170.004 0.141 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.006 99.4 49: (ns/day) (hour/ns) 49: Performance: 263.318 0.091 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.008 0.008 99.5 49: (ns/day) (hour/ns) 49: Performance: 190.330 0.126 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 99.4 49: (ns/day) (hour/ns) 49: Performance: 420.691 0.057 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 99.7 49: (ns/day) (hour/ns) 49: Performance: 283.624 0.085 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (86 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 97.7 49: (ns/day) (hour/ns) 49: Performance: 332.358 0.072 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.006 98.5 49: (ns/day) (hour/ns) 49: Performance: 226.985 0.106 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.1 49: (ns/day) (hour/ns) 49: Performance: 357.820 0.067 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.011 0.012 99.2 49: (ns/day) (hour/ns) 49: Performance: 127.169 0.189 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.2 49: (ns/day) (hour/ns) 49: Performance: 339.914 0.071 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 97.8 49: (ns/day) (hour/ns) 49: Performance: 430.359 0.056 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (77 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.3 49: (ns/day) (hour/ns) 49: Performance: 483.981 0.050 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 99.2 49: (ns/day) (hour/ns) 49: Performance: 371.568 0.065 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.8 49: (ns/day) (hour/ns) 49: Performance: 562.047 0.043 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 98.9 49: (ns/day) (hour/ns) 49: Performance: 505.008 0.048 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.004 98.4 49: (ns/day) (hour/ns) 49: Performance: 413.518 0.058 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.006 98.9 49: (ns/day) (hour/ns) 49: Performance: 255.679 0.094 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (57 ms) 49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.006 98.5 49: (ns/day) (hour/ns) 49: Performance: 263.577 0.091 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 98.7 49: (ns/day) (hour/ns) 49: Performance: 283.285 0.085 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.8 49: (ns/day) (hour/ns) 49: Performance: 356.826 0.067 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.003 0.003 97.9 49: (ns/day) (hour/ns) 49: Performance: 431.203 0.056 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.9 49: (ns/day) (hour/ns) 49: Performance: 360.479 0.067 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 1 of the 1 non-bonded parameter combinations 49: Excluding 1 bonded neighbours molecule type 'Argon' 49: Number of degrees of freedom in T-Coupling group System is 33.00 49: 49: There were 2 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'Argon' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.006 98.8 49: (ns/day) (hour/ns) 49: Performance: 230.199 0.104 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (71 ms) 49: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest (1541 ms total) 49: 49: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest 49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.5 49: (ns/day) (hour/ns) 49: Performance: 345.926 0.069 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.060 0.060 99.7 49: (ns/day) (hour/ns) 49: Performance: 24.349 0.986 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.039 0.039 99.8 49: (ns/day) (hour/ns) 49: Performance: 37.397 0.642 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.006 99.2 49: (ns/day) (hour/ns) 49: Performance: 237.576 0.101 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.007 0.007 98.7 49: (ns/day) (hour/ns) 49: Performance: 220.944 0.109 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.006 99.3 49: (ns/day) (hour/ns) 49: Performance: 245.471 0.098 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (3892 ms) 49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.008 0.009 98.2 49: (ns/day) (hour/ns) 49: Performance: 169.961 0.141 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.203 0.203 100.0 49: (ns/day) (hour/ns) 49: Performance: 7.236 3.317 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 98.7 49: (ns/day) (hour/ns) 49: Performance: 278.256 0.086 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.006 98.5 49: (ns/day) (hour/ns) 49: Performance: 229.916 0.104 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.024 0.024 99.6 49: (ns/day) (hour/ns) 49: Performance: 60.496 0.397 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.252 0.252 100.0 49: (ns/day) (hour/ns) 49: Performance: 5.817 4.126 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (4446 ms) 49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.175 0.175 99.9 49: (ns/day) (hour/ns) 49: Performance: 8.392 2.860 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 97.7 49: (ns/day) (hour/ns) 49: Performance: 375.875 0.064 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 98.2 49: (ns/day) (hour/ns) 49: Performance: 282.726 0.085 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 98.0 49: (ns/day) (hour/ns) 49: Performance: 327.918 0.073 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.319 0.319 100.0 49: (ns/day) (hour/ns) 49: Performance: 4.603 5.214 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.029 0.030 99.5 49: (ns/day) (hour/ns) 49: Performance: 49.775 0.482 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (4384 ms) 49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.131 0.131 99.9 49: (ns/day) (hour/ns) 49: Performance: 11.180 2.147 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.009 0.009 98.8 49: (ns/day) (hour/ns) 49: Performance: 156.277 0.154 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 98.3 49: (ns/day) (hour/ns) 49: Performance: 270.522 0.089 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.006 98.9 49: (ns/day) (hour/ns) 49: Performance: 254.465 0.094 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.019 0.019 99.5 49: (ns/day) (hour/ns) 49: Performance: 76.226 0.315 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.007 98.3 49: (ns/day) (hour/ns) 49: Performance: 224.880 0.107 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (4210 ms) 49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 97.8 49: (ns/day) (hour/ns) 49: Performance: 268.845 0.089 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 97.9 49: (ns/day) (hour/ns) 49: Performance: 342.274 0.070 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.006 98.1 49: (ns/day) (hour/ns) 49: Performance: 252.939 0.095 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.006 98.4 49: (ns/day) (hour/ns) 49: Performance: 264.426 0.091 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 97.9 49: (ns/day) (hour/ns) 49: Performance: 329.338 0.073 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 98.4 49: (ns/day) (hour/ns) 49: Performance: 278.269 0.086 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (4511 ms) 49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.061 0.061 99.7 49: (ns/day) (hour/ns) 49: Performance: 24.185 0.992 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 97.9 49: (ns/day) (hour/ns) 49: Performance: 368.258 0.065 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.009 0.010 98.9 49: (ns/day) (hour/ns) 49: Performance: 153.191 0.157 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 98.4 49: (ns/day) (hour/ns) 49: Performance: 268.155 0.090 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.006 98.4 49: (ns/day) (hour/ns) 49: Performance: 243.069 0.099 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 98.3 49: (ns/day) (hour/ns) 49: Performance: 304.452 0.079 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (4008 ms) 49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 99.4 49: (ns/day) (hour/ns) 49: Performance: 303.822 0.079 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 99.3 49: (ns/day) (hour/ns) 49: Performance: 269.528 0.089 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 99.3 49: (ns/day) (hour/ns) 49: Performance: 298.580 0.080 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 99.3 49: (ns/day) (hour/ns) 49: Performance: 305.101 0.079 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.006 0.006 99.1 49: (ns/day) (hour/ns) 49: Performance: 228.636 0.105 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: NVE simulation: will use the initial temperature of 398.997 K for 49: determining the Verlet buffer size 49: 49: 49: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Can not increase nstlist because an NVE ensemble is used 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.004 0.004 99.3 49: (ns/day) (hour/ns) 49: Performance: 355.057 0.068 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (4338 ms) 49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 99.1 49: (ns/day) (hour/ns) 49: Performance: 321.383 0.075 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.007 0.007 99.6 49: (ns/day) (hour/ns) 49: Performance: 215.150 0.112 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 99.4 49: (ns/day) (hour/ns) 49: Performance: 321.400 0.075 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 49: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.007 0.007 99.4 49: (ns/day) (hour/ns) 49: Performance: 219.613 0.109 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.007 0.007 99.5 49: (ns/day) (hour/ns) 49: Performance: 206.233 0.116 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 49: 49: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 49: that with the Verlet scheme, nstlist has no effect on the accuracy of 49: your simulation. 49: 49: 49: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (4) 49: 49: Generated 330891 of the 330891 non-bonded parameter combinations 49: Generating 1-4 interactions: fudge = 0.5 49: Generated 330891 of the 330891 1-4 parameter combinations 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: Number of degrees of freedom in T-Coupling group System is 27.00 49: 49: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 3 notes 49: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 49: log). 49: The current CPU can measure timings more accurately than the code in 49: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 49: speed as accurate timings are needed for load-balancing. 49: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 49: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 49: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 49: 49: 49: Using 1 MPI thread 49: 49: Non-default thread affinity set, disabling internal thread affinity 49: 49: Using 1 OpenMP thread 49: 49: starting mdrun 'spc2' 49: 16 steps, 0.0 ps. 49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: This run will generate roughly 0 Mb of data 49: 49: Writing final coordinates. 49: 49: Core t (s) Wall t (s) (%) 49: Time: 0.005 0.005 99.4 49: (ns/day) (hour/ns) 49: Performance: 295.288 0.081 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 49: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (4159 ms) 49: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest (33948 ms total) 49: 49: [----------] Global test environment tear-down 49: [==========] 27 tests from 3 test cases ran. (35619 ms total) 49: [ PASSED ] 27 tests. 49/54 Test #49: MdrunMpiCoordinationTestsOneRank .... Passed 35.63 sec test 50 Start 50: MdrunMpiCoordinationTestsTwoRanks 50: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/mdrun-mpi-coordination-test "-ntmpi" "2" "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/MdrunMpiCoordinationTestsTwoRanks.xml" 50: Test timeout computed to be: 960 50: [==========] Running 27 tests from 3 test cases. 50: [----------] Global test environment set-up. 50: [----------] 1 test from BasicPropagators/PeriodicActionsTest 50: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was turned on during the run due to measured imbalance. 50: Average load imbalance: 13.7%. 50: The balanceable part of the MD step is 43%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 5.9%. 50: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 50: 50: NOTE: 5.9 % of the available CPU time was lost due to load imbalance 50: in the domain decomposition. 50: You can consider manually changing the decomposition (option -dd); 50: e.g. by using fewer domains along the box dimension in which there is 50: considerable inhomogeneity in the simulated system. 50: 50: NOTE: 41 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.012 0.006 195.8 50: (ns/day) (hour/ns) 50: Performance: 239.372 0.100 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 3.2%. 50: The balanceable part of the MD step is 42%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.3%. 50: 50: 50: NOTE: 40 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.005 195.2 50: (ns/day) (hour/ns) 50: Performance: 304.731 0.079 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.2%. 50: The balanceable part of the MD step is 29%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.4%. 50: 50: 50: NOTE: 40 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.003 196.2 50: (ns/day) (hour/ns) 50: Performance: 434.074 0.055 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 10.9%. 50: The balanceable part of the MD step is 17%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.9%. 50: 50: 50: NOTE: 27 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.014 0.007 196.8 50: (ns/day) (hour/ns) 50: Performance: 207.595 0.116 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was turned on during the run due to measured imbalance. 50: Average load imbalance: 4.7%. 50: The balanceable part of the MD step is 49%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 2.3%. 50: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 50: 50: 50: NOTE: 42 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.010 0.005 196.2 50: (ns/day) (hour/ns) 50: Performance: 294.681 0.081 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was turned on during the run due to measured imbalance. 50: Average load imbalance: 5.7%. 50: The balanceable part of the MD step is 50%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 2.8%. 50: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 50: 50: 50: NOTE: 39 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.004 197.0 50: (ns/day) (hour/ns) 50: Performance: 388.779 0.062 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 50: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (186 ms) 50: [----------] 1 test from BasicPropagators/PeriodicActionsTest (186 ms total) 50: 50: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 3.2%. 50: The balanceable part of the MD step is 26%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.8%. 50: 50: 50: NOTE: 48 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.099 0.049 199.4 50: (ns/day) (hour/ns) 50: Performance: 29.729 0.807 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.0%. 50: The balanceable part of the MD step is 52%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.5%. 50: 50: 50: NOTE: 40 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.010 0.005 194.9 50: (ns/day) (hour/ns) 50: Performance: 274.090 0.088 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.6%. 50: The balanceable part of the MD step is 49%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.3%. 50: 50: 50: NOTE: 42 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.011 0.006 195.9 50: (ns/day) (hour/ns) 50: Performance: 262.248 0.092 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was turned on during the run due to measured imbalance. 50: Average load imbalance: 4.0%. 50: The balanceable part of the MD step is 51%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 2.0%. 50: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 50: 50: 50: NOTE: 42 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.010 0.005 196.5 50: (ns/day) (hour/ns) 50: Performance: 278.836 0.086 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 0.6%. 50: The balanceable part of the MD step is 53%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.3%. 50: 50: 50: NOTE: 93 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.092 0.046 199.3 50: (ns/day) (hour/ns) 50: Performance: 31.835 0.754 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 3.4%. 50: The balanceable part of the MD step is 50%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.7%. 50: 50: 50: NOTE: 45 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.019 0.010 195.0 50: (ns/day) (hour/ns) 50: Performance: 148.211 0.162 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (182 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was turned on during the run due to measured imbalance. 50: Average load imbalance: 6.6%. 50: The balanceable part of the MD step is 50%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 3.3%. 50: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 50: 50: 50: NOTE: 44 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.014 0.007 194.7 50: (ns/day) (hour/ns) 50: Performance: 198.835 0.121 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was turned on during the run due to measured imbalance. 50: Average load imbalance: 6.0%. 50: The balanceable part of the MD step is 49%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 2.9%. 50: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 50: 50: 50: NOTE: 90 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.105 0.053 198.9 50: (ns/day) (hour/ns) 50: Performance: 27.843 0.862 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was turned on during the run due to measured imbalance. 50: Average load imbalance: 5.5%. 50: The balanceable part of the MD step is 50%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 2.8%. 50: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 50: 50: 50: NOTE: 44 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.016 0.008 194.9 50: (ns/day) (hour/ns) 50: Performance: 180.787 0.133 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.0%. 50: The balanceable part of the MD step is 43%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.9%. 50: 50: 50: NOTE: 49 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.106 0.053 199.0 50: (ns/day) (hour/ns) 50: Performance: 27.465 0.874 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.0%. 50: The balanceable part of the MD step is 43%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.4%. 50: 50: 50: NOTE: 40 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.005 194.4 50: (ns/day) (hour/ns) 50: Performance: 318.550 0.075 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.0%. 50: The balanceable part of the MD step is 53%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.5%. 50: 50: 50: NOTE: 39 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.010 0.005 194.9 50: (ns/day) (hour/ns) 50: Performance: 300.246 0.080 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (214 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was turned on during the run due to measured imbalance. 50: Average load imbalance: 5.1%. 50: The balanceable part of the MD step is 50%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 2.5%. 50: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 50: 50: 50: NOTE: 42 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.013 0.007 193.2 50: (ns/day) (hour/ns) 50: Performance: 218.880 0.110 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.4%. 50: The balanceable part of the MD step is 7%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.1%. 50: 50: 50: NOTE: 19 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.025 0.013 197.4 50: (ns/day) (hour/ns) 50: Performance: 115.131 0.208 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.4%. 50: The balanceable part of the MD step is 51%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.7%. 50: 50: 50: NOTE: 42 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 194.2 50: (ns/day) (hour/ns) 50: Performance: 352.719 0.068 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was turned on during the run due to measured imbalance. 50: Average load imbalance: 7.0%. 50: The balanceable part of the MD step is 42%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 3.0%. 50: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 50: 50: 50: NOTE: 40 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.011 0.006 196.1 50: (ns/day) (hour/ns) 50: Performance: 256.948 0.093 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.3%. 50: The balanceable part of the MD step is 51%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.2%. 50: 50: 50: NOTE: 92 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.091 0.046 199.0 50: (ns/day) (hour/ns) 50: Performance: 32.018 0.750 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.9%. 50: The balanceable part of the MD step is 34%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.6%. 50: 50: 50: NOTE: 38 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.015 0.008 196.4 50: (ns/day) (hour/ns) 50: Performance: 195.814 0.123 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (190 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 41 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 196.1 50: (ns/day) (hour/ns) 50: Performance: 351.161 0.068 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 43 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 197.0 50: (ns/day) (hour/ns) 50: Performance: 363.414 0.066 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 49 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.102 0.051 199.7 50: (ns/day) (hour/ns) 50: Performance: 28.849 0.832 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 42 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.010 0.005 196.0 50: (ns/day) (hour/ns) 50: Performance: 288.870 0.083 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 40 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 195.8 50: (ns/day) (hour/ns) 50: Performance: 375.268 0.064 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 41 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 196.0 50: (ns/day) (hour/ns) 50: Performance: 381.296 0.063 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (120 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 49 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.101 0.051 199.6 50: (ns/day) (hour/ns) 50: Performance: 28.912 0.830 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 39 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.010 0.005 197.4 50: (ns/day) (hour/ns) 50: Performance: 304.204 0.079 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 37 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.012 0.006 192.6 50: (ns/day) (hour/ns) 50: Performance: 233.325 0.103 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 39 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.010 0.005 194.7 50: (ns/day) (hour/ns) 50: Performance: 274.493 0.087 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 35 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.010 0.005 193.4 50: (ns/day) (hour/ns) 50: Performance: 272.273 0.088 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 42 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.010 0.005 196.7 50: (ns/day) (hour/ns) 50: Performance: 296.047 0.081 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (181 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 41 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.012 0.006 195.5 50: (ns/day) (hour/ns) 50: Performance: 241.129 0.100 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 49 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.112 0.056 199.5 50: (ns/day) (hour/ns) 50: Performance: 26.127 0.919 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 41 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.012 0.006 195.1 50: (ns/day) (hour/ns) 50: Performance: 236.664 0.101 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 41 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.012 0.006 196.5 50: (ns/day) (hour/ns) 50: Performance: 239.651 0.100 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 42 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.011 0.006 194.1 50: (ns/day) (hour/ns) 50: Performance: 262.075 0.092 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 43 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.014 0.007 196.6 50: (ns/day) (hour/ns) 50: Performance: 204.034 0.118 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (199 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 42 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.005 191.1 50: (ns/day) (hour/ns) 50: Performance: 305.646 0.079 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 7 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.045 19.1 50: (ns/day) (hour/ns) 50: Performance: 32.539 0.738 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 39 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.014 0.007 197.8 50: (ns/day) (hour/ns) 50: Performance: 210.579 0.114 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 41 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 197.5 50: (ns/day) (hour/ns) 50: Performance: 348.983 0.069 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 44 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.012 0.006 196.4 50: (ns/day) (hour/ns) 50: Performance: 247.946 0.097 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 41 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.014 0.007 197.9 50: (ns/day) (hour/ns) 50: Performance: 201.300 0.119 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (188 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: 50: WARNING 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Using Berendsen pressure coupling invalidates the true ensemble for the 50: thermostat 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: 50: There was 1 warning 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 42 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.016 0.008 196.9 50: (ns/day) (hour/ns) 50: Performance: 177.380 0.135 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: 50: WARNING 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Using Berendsen pressure coupling invalidates the true ensemble for the 50: thermostat 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: 50: There was 1 warning 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 44 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.017 0.009 196.2 50: (ns/day) (hour/ns) 50: Performance: 167.544 0.143 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: 50: WARNING 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Using Berendsen pressure coupling invalidates the true ensemble for the 50: thermostat 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: 50: There was 1 warning 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 45 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.018 0.009 198.0 50: (ns/day) (hour/ns) 50: Performance: 165.250 0.145 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: 50: WARNING 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Using Berendsen pressure coupling invalidates the true ensemble for the 50: thermostat 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: 50: There was 1 warning 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 41 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.005 196.6 50: (ns/day) (hour/ns) 50: Performance: 313.644 0.077 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: 50: WARNING 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Using Berendsen pressure coupling invalidates the true ensemble for the 50: thermostat 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: 50: There was 1 warning 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 44 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.013 0.007 195.8 50: (ns/day) (hour/ns) 50: Performance: 222.031 0.108 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: 50: WARNING 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Using Berendsen pressure coupling invalidates the true ensemble for the 50: thermostat 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: 50: There was 1 warning 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 49 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.093 0.047 199.3 50: (ns/day) (hour/ns) 50: Performance: 31.424 0.764 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (191 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 40 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 196.1 50: (ns/day) (hour/ns) 50: Performance: 374.322 0.064 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 42 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.004 195.5 50: (ns/day) (hour/ns) 50: Performance: 328.232 0.073 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 41 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.010 0.005 197.8 50: (ns/day) (hour/ns) 50: Performance: 298.529 0.080 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 49 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.090 0.045 199.5 50: (ns/day) (hour/ns) 50: Performance: 32.487 0.739 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 43 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.005 195.4 50: (ns/day) (hour/ns) 50: Performance: 323.069 0.074 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 40 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.004 195.2 50: (ns/day) (hour/ns) 50: Performance: 332.762 0.072 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (124 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 41 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.005 197.2 50: (ns/day) (hour/ns) 50: Performance: 308.130 0.078 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 41 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.004 196.5 50: (ns/day) (hour/ns) 50: Performance: 338.243 0.071 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 44 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.017 0.009 194.7 50: (ns/day) (hour/ns) 50: Performance: 164.748 0.146 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 41 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.004 196.3 50: (ns/day) (hour/ns) 50: Performance: 384.544 0.062 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 41 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 196.3 50: (ns/day) (hour/ns) 50: Performance: 359.082 0.067 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 43 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.010 0.005 196.5 50: (ns/day) (hour/ns) 50: Performance: 303.336 0.079 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (123 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 45 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.017 0.009 196.9 50: (ns/day) (hour/ns) 50: Performance: 171.230 0.140 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 42 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.011 0.006 196.1 50: (ns/day) (hour/ns) 50: Performance: 263.628 0.091 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 41 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 196.8 50: (ns/day) (hour/ns) 50: Performance: 357.810 0.067 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 45 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.011 0.005 197.3 50: (ns/day) (hour/ns) 50: Performance: 273.215 0.088 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 38 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.012 0.006 196.1 50: (ns/day) (hour/ns) 50: Performance: 243.478 0.099 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 44 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.012 0.006 196.6 50: (ns/day) (hour/ns) 50: Performance: 233.219 0.103 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (172 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 38 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 195.7 50: (ns/day) (hour/ns) 50: Performance: 365.864 0.066 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 42 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.005 195.5 50: (ns/day) (hour/ns) 50: Performance: 306.543 0.078 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 49 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.092 0.046 199.6 50: (ns/day) (hour/ns) 50: Performance: 31.719 0.757 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 42 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.011 0.006 196.1 50: (ns/day) (hour/ns) 50: Performance: 254.691 0.094 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 40 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.012 0.006 196.6 50: (ns/day) (hour/ns) 50: Performance: 234.994 0.102 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 39 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 192.6 50: (ns/day) (hour/ns) 50: Performance: 349.696 0.069 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (131 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 7.9%. 50: The balanceable part of the MD step is 15%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.1%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.022 0.011 195.0 50: (ns/day) (hour/ns) 50: Performance: 129.750 0.185 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 0.4%. 50: The balanceable part of the MD step is 49%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.2%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.014 0.007 196.3 50: (ns/day) (hour/ns) 50: Performance: 204.896 0.117 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.4%. 50: The balanceable part of the MD step is 31%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.4%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.010 0.005 194.5 50: (ns/day) (hour/ns) 50: Performance: 277.529 0.086 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 0.9%. 50: The balanceable part of the MD step is 57%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.5%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.012 0.006 194.6 50: (ns/day) (hour/ns) 50: Performance: 231.466 0.104 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.4%. 50: The balanceable part of the MD step is 44%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.1%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.016 0.008 190.0 50: (ns/day) (hour/ns) 50: Performance: 176.653 0.136 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was turned on during the run due to measured imbalance. 50: Average load imbalance: 4.7%. 50: The balanceable part of the MD step is 47%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 2.2%. 50: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.015 0.008 195.4 50: (ns/day) (hour/ns) 50: Performance: 187.289 0.128 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (178 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 0.7%. 50: The balanceable part of the MD step is 43%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.3%. 50: 50: 50: NOTE: 41 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.011 0.006 190.2 50: (ns/day) (hour/ns) 50: Performance: 262.824 0.091 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.1%. 50: The balanceable part of the MD step is 57%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.2%. 50: 50: 50: NOTE: 95 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.089 0.045 199.3 50: (ns/day) (hour/ns) 50: Performance: 32.866 0.730 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 0.4%. 50: The balanceable part of the MD step is 46%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.2%. 50: 50: 50: NOTE: 39 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.010 0.005 196.3 50: (ns/day) (hour/ns) 50: Performance: 279.348 0.086 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.7%. 50: The balanceable part of the MD step is 53%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.4%. 50: 50: 50: NOTE: 39 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.005 196.0 50: (ns/day) (hour/ns) 50: Performance: 305.775 0.078 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 0.5%. 50: The balanceable part of the MD step is 37%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.2%. 50: 50: 50: NOTE: 40 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.011 0.006 197.8 50: (ns/day) (hour/ns) 50: Performance: 255.308 0.094 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 50: NVE simulation: will use the initial temperature of 68.810 K for 50: determining the Verlet buffer size 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 7.6%. 50: The balanceable part of the MD step is 2%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.1%. 50: 50: 50: NOTE: 6 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.100 0.050 198.7 50: (ns/day) (hour/ns) 50: Performance: 29.242 0.821 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (177 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.012 0.006 195.6 50: (ns/day) (hour/ns) 50: Performance: 246.315 0.097 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 193.5 50: (ns/day) (hour/ns) 50: Performance: 336.930 0.071 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.011 0.006 194.7 50: (ns/day) (hour/ns) 50: Performance: 248.913 0.096 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.020 0.010 192.9 50: (ns/day) (hour/ns) 50: Performance: 144.165 0.166 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.010 0.005 190.3 50: (ns/day) (hour/ns) 50: Performance: 267.190 0.090 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.013 0.007 192.2 50: (ns/day) (hour/ns) 50: Performance: 222.163 0.108 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (140 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 41 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.023 0.012 198.0 50: (ns/day) (hour/ns) 50: Performance: 125.734 0.191 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 41 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.014 0.007 197.6 50: (ns/day) (hour/ns) 50: Performance: 214.017 0.112 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 49 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.129 0.065 199.3 50: (ns/day) (hour/ns) 50: Performance: 22.762 1.054 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 37 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.013 0.006 195.2 50: (ns/day) (hour/ns) 50: Performance: 228.373 0.105 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 37 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.014 0.008 187.2 50: (ns/day) (hour/ns) 50: Performance: 194.808 0.123 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 49 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.088 0.044 199.5 50: (ns/day) (hour/ns) 50: Performance: 33.392 0.719 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (257 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 39 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.005 194.4 50: (ns/day) (hour/ns) 50: Performance: 305.207 0.079 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 36 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.014 0.007 195.7 50: (ns/day) (hour/ns) 50: Performance: 205.336 0.117 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 40 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.012 0.006 196.0 50: (ns/day) (hour/ns) 50: Performance: 231.675 0.104 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 44 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.024 0.012 198.1 50: (ns/day) (hour/ns) 50: Performance: 122.020 0.197 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 40 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.010 0.005 196.7 50: (ns/day) (hour/ns) 50: Performance: 291.715 0.082 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 38 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.005 196.8 50: (ns/day) (hour/ns) 50: Performance: 316.220 0.076 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (136 ms) 50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 43 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.016 0.008 197.5 50: (ns/day) (hour/ns) 50: Performance: 183.201 0.131 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 39 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.014 0.007 183.0 50: (ns/day) (hour/ns) 50: Performance: 198.549 0.121 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 42 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.016 0.008 196.0 50: (ns/day) (hour/ns) 50: Performance: 180.923 0.133 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 43 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.013 0.007 196.0 50: (ns/day) (hour/ns) 50: Performance: 217.209 0.110 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 90 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.087 0.043 199.5 50: (ns/day) (hour/ns) 50: Performance: 33.852 0.709 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 1 of the 1 non-bonded parameter combinations 50: Excluding 1 bonded neighbours molecule type 'Argon' 50: Number of degrees of freedom in T-Coupling group System is 33.00 50: 50: There were 2 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'Argon' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: NOTE: 42 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.019 0.010 193.3 50: (ns/day) (hour/ns) 50: Performance: 148.505 0.162 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (183 ms) 50: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest (3087 ms total) 50: 50: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest 50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 4.3%. 50: The balanceable part of the MD step is 2%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.1%. 50: 50: 50: NOTE: 30 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.154 0.089 171.9 50: (ns/day) (hour/ns) 50: Performance: 16.434 1.460 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 3.6%. 50: The balanceable part of the MD step is 37%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.3%. 50: 50: 50: NOTE: 40 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.004 196.3 50: (ns/day) (hour/ns) 50: Performance: 408.446 0.059 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB got disabled because it was unsuitable to use. 50: Average load imbalance: 6.0%. 50: The balanceable part of the MD step is 51%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 3.0%. 50: 50: 50: NOTE: 42 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.014 0.007 198.0 50: (ns/day) (hour/ns) 50: Performance: 214.793 0.112 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.6%. 50: The balanceable part of the MD step is 53%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.8%. 50: 50: 50: NOTE: 38 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 195.4 50: (ns/day) (hour/ns) 50: Performance: 359.879 0.067 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 3.3%. 50: The balanceable part of the MD step is 40%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.3%. 50: 50: 50: NOTE: 40 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.013 0.007 197.2 50: (ns/day) (hour/ns) 50: Performance: 221.632 0.108 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.8%. 50: The balanceable part of the MD step is 51%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.9%. 50: 50: 50: NOTE: 78 % of the run time was spent in domain decomposition, 50: 0 % of the run time was spent in pair search, 50: you might want to increase nstlist (this has no effect on accuracy) 50: 50: NOTE: 10 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.064 0.032 199.2 50: (ns/day) (hour/ns) 50: Performance: 46.024 0.521 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (4891 ms) 50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.6%. 50: The balanceable part of the MD step is 41%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.7%. 50: 50: 50: NOTE: 38 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.011 0.005 194.6 50: (ns/day) (hour/ns) 50: Performance: 268.500 0.089 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.8%. 50: The balanceable part of the MD step is 54%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.5%. 50: 50: 50: NOTE: 49 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.130 0.065 199.6 50: (ns/day) (hour/ns) 50: Performance: 22.576 1.063 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.5%. 50: The balanceable part of the MD step is 44%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.1%. 50: 50: 50: NOTE: 41 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.013 0.007 193.3 50: (ns/day) (hour/ns) 50: Performance: 216.435 0.111 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.0%. 50: The balanceable part of the MD step is 43%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.9%. 50: 50: 50: NOTE: 40 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.011 0.006 195.8 50: (ns/day) (hour/ns) 50: Performance: 258.447 0.093 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.7%. 50: The balanceable part of the MD step is 52%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.9%. 50: 50: 50: NOTE: 48 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.053 0.027 199.2 50: (ns/day) (hour/ns) 50: Performance: 54.851 0.438 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 0.7%. 50: The balanceable part of the MD step is 53%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.4%. 50: 50: 50: NOTE: 40 % of the run time was spent communicating energies, 50: you might want to increase some nst* mdp options 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 195.8 50: (ns/day) (hour/ns) 50: Performance: 350.921 0.068 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (4433 ms) 50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.056 0.028 199.0 50: (ns/day) (hour/ns) 50: Performance: 52.251 0.459 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.013 0.006 196.6 50: (ns/day) (hour/ns) 50: Performance: 228.500 0.105 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.013 0.007 197.3 50: (ns/day) (hour/ns) 50: Performance: 219.527 0.109 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 195.1 50: (ns/day) (hour/ns) 50: Performance: 343.151 0.070 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.010 0.005 191.3 50: (ns/day) (hour/ns) 50: Performance: 293.271 0.082 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.007 0.004 196.2 50: (ns/day) (hour/ns) 50: Performance: 403.841 0.059 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (3993 ms) 50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.004 192.8 50: (ns/day) (hour/ns) 50: Performance: 330.194 0.073 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.004 195.5 50: (ns/day) (hour/ns) 50: Performance: 331.598 0.072 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.012 0.006 195.9 50: (ns/day) (hour/ns) 50: Performance: 245.086 0.098 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.017 0.009 195.8 50: (ns/day) (hour/ns) 50: Performance: 171.839 0.140 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.010 0.005 196.5 50: (ns/day) (hour/ns) 50: Performance: 292.297 0.082 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.012 0.006 195.4 50: (ns/day) (hour/ns) 50: Performance: 245.212 0.098 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (3967 ms) 50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 195.6 50: (ns/day) (hour/ns) 50: Performance: 377.314 0.064 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.012 0.006 197.2 50: (ns/day) (hour/ns) 50: Performance: 248.131 0.097 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 195.6 50: (ns/day) (hour/ns) 50: Performance: 364.834 0.066 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.010 0.005 197.0 50: (ns/day) (hour/ns) 50: Performance: 295.217 0.081 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.005 195.7 50: (ns/day) (hour/ns) 50: Performance: 307.476 0.078 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.544 0.272 199.9 50: (ns/day) (hour/ns) 50: Performance: 5.400 4.445 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (3891 ms) 50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.013 0.006 196.2 50: (ns/day) (hour/ns) 50: Performance: 227.972 0.105 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.010 0.005 196.1 50: (ns/day) (hour/ns) 50: Performance: 299.414 0.080 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.004 196.1 50: (ns/day) (hour/ns) 50: Performance: 334.797 0.072 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 191.2 50: (ns/day) (hour/ns) 50: Performance: 369.119 0.065 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.005 196.9 50: (ns/day) (hour/ns) 50: Performance: 314.838 0.076 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.005 196.3 50: (ns/day) (hour/ns) 50: Performance: 322.865 0.074 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (3761 ms) 50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.3%. 50: The balanceable part of the MD step is 55%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.7%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 193.4 50: (ns/day) (hour/ns) 50: Performance: 337.013 0.071 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 1.9%. 50: The balanceable part of the MD step is 59%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.1%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.008 0.004 194.4 50: (ns/day) (hour/ns) 50: Performance: 360.037 0.067 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB got disabled because it was unsuitable to use. 50: Average load imbalance: 5.8%. 50: The balanceable part of the MD step is 57%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 3.3%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.019 0.010 197.0 50: (ns/day) (hour/ns) 50: Performance: 150.337 0.160 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 4.1%. 50: The balanceable part of the MD step is 47%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.9%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.012 0.006 192.0 50: (ns/day) (hour/ns) 50: Performance: 241.910 0.099 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.2%. 50: The balanceable part of the MD step is 4%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 0.1%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.073 0.037 199.2 50: (ns/day) (hour/ns) 50: Performance: 40.013 0.600 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: NVE simulation: will use the initial temperature of 398.997 K for 50: determining the Verlet buffer size 50: 50: 50: NOTE 4 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 4 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Can not increase nstlist because an NVE ensemble is used 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: 50: Dynamic load balancing report: 50: DLB was off during the run due to low measured imbalance. 50: Average load imbalance: 2.9%. 50: The balanceable part of the MD step is 53%, load imbalance is computed from this. 50: Part of the total run time spent waiting due to load imbalance: 1.5%. 50: 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.005 193.7 50: (ns/day) (hour/ns) 50: Performance: 306.833 0.078 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (4145 ms) 50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.096 0.048 199.4 50: (ns/day) (hour/ns) 50: Performance: 30.387 0.790 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.070 0.035 199.0 50: (ns/day) (hour/ns) 50: Performance: 41.504 0.578 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.005 192.1 50: (ns/day) (hour/ns) 50: Performance: 305.003 0.079 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 50: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.005 190.4 50: (ns/day) (hour/ns) 50: Performance: 297.455 0.081 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.014 0.007 194.1 50: (ns/day) (hour/ns) 50: Performance: 208.791 0.115 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 50: 50: NOTE 1 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 50: that with the Verlet scheme, nstlist has no effect on the accuracy of 50: your simulation. 50: 50: 50: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: Setting nstcalcenergy (100) equal to nstenergy (4) 50: 50: Generated 330891 of the 330891 non-bonded parameter combinations 50: Generating 1-4 interactions: fudge = 0.5 50: Generated 330891 of the 330891 1-4 parameter combinations 50: Excluding 2 bonded neighbours molecule type 'SOL' 50: Number of degrees of freedom in T-Coupling group System is 27.00 50: 50: NOTE 3 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 50: You are using a plain Coulomb cut-off, which might produce artifacts. 50: You might want to consider using PME electrostatics. 50: 50: 50: 50: There were 3 notes 50: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 50: log). 50: The current CPU can measure timings more accurately than the code in 50: mdrun-mpi-coordination-test was configured to use. This might affect your simulation 50: speed as accurate timings are needed for load-balancing. 50: Please consider rebuilding mdrun-mpi-coordination-test with the GMX_USE_RDTSCP=ON CMake option. 50: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 50: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 50: 50: 50: Using 2 MPI threads 50: Using 1 OpenMP thread per tMPI thread 50: 50: 50: NOTE: The number of threads is not equal to the number of (logical) cores 50: and the -pin option is set to auto: will not pin threads to cores. 50: This can lead to significant performance degradation. 50: Consider using -pin on (and -pinoffset in case you run multiple jobs). 50: starting mdrun 'spc2' 50: 16 steps, 0.0 ps. 50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 50: Note that mdrun will redetermine rlist based on the actual pair-list setup 50: This run will generate roughly 0 Mb of data 50: 50: Writing final coordinates. 50: 50: Core t (s) Wall t (s) (%) 50: Time: 0.009 0.005 192.9 50: (ns/day) (hour/ns) 50: Performance: 306.734 0.078 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 50: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (3900 ms) 50: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest (32982 ms total) 50: 50: [----------] Global test environment tear-down 50: [==========] 27 tests from 3 test cases ran. (36255 ms total) 50: [ PASSED ] 27 tests. 50/54 Test #50: MdrunMpiCoordinationTestsTwoRanks ... Passed 36.27 sec test 51 Start 51: GmxapiExternalInterfaceTests 51: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/GmxapiExternalInterfaceTests.xml" 51: Test timeout computed to be: 600 51: [==========] Running 9 tests from 2 test cases. 51: [----------] Global test environment set-up. 51: [----------] 8 tests from GmxApiTest 51: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD 51: Setting the LD random seed to -1073795081 51: Generated 331705 of the 331705 non-bonded parameter combinations 51: Generating 1-4 interactions: fudge = 0.5 51: Generated 331705 of the 331705 1-4 parameter combinations 51: Excluding 2 bonded neighbours molecule type 'SOL' 51: Excluding 3 bonded neighbours molecule type 'methane' 51: 51: NOTE 1 [file spc_and_methane.top, line 33]: 51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 51: the time step of 2.0e-03 ps. 51: Maybe you forgot to change the constraints mdp option. 51: 51: Number of degrees of freedom in T-Coupling group System is 18.00 51: 51: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 51: You are using a plain Coulomb cut-off, which might produce artifacts. 51: You might want to consider using PME electrostatics. 51: 51: 51: 51: There were 2 notes 51: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 51: log). 51: The current CPU can measure timings more accurately than the code in 51: gmxapi-test was configured to use. This might affect your simulation 51: speed as accurate timings are needed for load-balancing. 51: Please consider rebuilding gmxapi-test with the GMX_USE_RDTSCP=ON CMake option. 51: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.309 51: 51: 51: Using 1 MPI thread 51: 51: Non-default thread affinity set, disabling internal thread affinity 51: 51: Using 2 OpenMP threads 51: 51: starting mdrun 'Water and methane' 51: 2 steps, 0.0 ps. 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: This run will generate roughly 0 Mb of data 51: 51: Writing final coordinates. 51: 51: Core t (s) Wall t (s) (%) 51: Time: 1.033 0.517 200.0 51: (ns/day) (hour/ns) 51: Performance: 0.980 24.502 51: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (1292 ms) 51: [ RUN ] GmxApiTest.SystemConstruction 51: Setting the LD random seed to -1150305029 51: Generated 331705 of the 331705 non-bonded parameter combinations 51: Generating 1-4 interactions: fudge = 0.5 51: Generated 331705 of the 331705 1-4 parameter combinations 51: Excluding 2 bonded neighbours molecule type 'SOL' 51: Excluding 3 bonded neighbours molecule type 'methane' 51: 51: NOTE 1 [file spc_and_methane.top, line 33]: 51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 51: the time step of 2.0e-03 ps. 51: Maybe you forgot to change the constraints mdp option. 51: 51: Number of degrees of freedom in T-Coupling group System is 18.00 51: 51: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 51: You are using a plain Coulomb cut-off, which might produce artifacts. 51: You might want to consider using PME electrostatics. 51: 51: 51: 51: There were 2 notes 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: This run will generate roughly 0 Mb of data 51: [ OK ] GmxApiTest.SystemConstruction (622 ms) 51: [ RUN ] GmxApiTest.SaneVersionComparisons 51: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) 51: [ RUN ] GmxApiTest.VersionNamed0_1_Features 51: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) 51: [ RUN ] GmxApiTest.RunnerBasicMD 51: Setting the LD random seed to 1537195997 51: Generated 331705 of the 331705 non-bonded parameter combinations 51: Generating 1-4 interactions: fudge = 0.5 51: Generated 331705 of the 331705 1-4 parameter combinations 51: Excluding 2 bonded neighbours molecule type 'SOL' 51: Excluding 3 bonded neighbours molecule type 'methane' 51: 51: NOTE 1 [file spc_and_methane.top, line 33]: 51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 51: the time step of 2.0e-03 ps. 51: Maybe you forgot to change the constraints mdp option. 51: 51: Number of degrees of freedom in T-Coupling group System is 18.00 51: 51: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 51: You are using a plain Coulomb cut-off, which might produce artifacts. 51: You might want to consider using PME electrostatics. 51: 51: 51: 51: There were 2 notes 51: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 51: log). 51: The current CPU can measure timings more accurately than the code in 51: gmxapi-test was configured to use. This might affect your simulation 51: speed as accurate timings are needed for load-balancing. 51: Please consider rebuilding gmxapi-test with the GMX_USE_RDTSCP=ON CMake option. 51: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.309 51: 51: 51: Using 1 MPI thread 51: 51: Non-default thread affinity set, disabling internal thread affinity 51: 51: Using 2 OpenMP threads 51: 51: starting mdrun 'Water and methane' 51: 2 steps, 0.0 ps. 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: This run will generate roughly 0 Mb of data 51: 51: Writing final coordinates. 51: 51: Core t (s) Wall t (s) (%) 51: Time: 0.007 0.003 196.3 51: (ns/day) (hour/ns) 51: Performance: 147.048 0.163 51: [ OK ] GmxApiTest.RunnerBasicMD (601 ms) 51: [ RUN ] GmxApiTest.RunnerReinitialize 51: Setting the LD random seed to -541475093 51: Generated 331705 of the 331705 non-bonded parameter combinations 51: Generating 1-4 interactions: fudge = 0.5 51: Generated 331705 of the 331705 1-4 parameter combinations 51: Excluding 2 bonded neighbours molecule type 'SOL' 51: Excluding 3 bonded neighbours molecule type 'methane' 51: 51: NOTE 1 [file spc_and_methane.top, line 33]: 51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 51: the time step of 2.0e-03 ps. 51: Maybe you forgot to change the constraints mdp option. 51: 51: Number of degrees of freedom in T-Coupling group System is 18.00 51: 51: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 51: You are using a plain Coulomb cut-off, which might produce artifacts. 51: You might want to consider using PME electrostatics. 51: 51: 51: 51: There were 2 notes 51: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 51: log). 51: The current CPU can measure timings more accurately than the code in 51: gmxapi-test was configured to use. This might affect your simulation 51: speed as accurate timings are needed for load-balancing. 51: Please consider rebuilding gmxapi-test with the GMX_USE_RDTSCP=ON CMake option. 51: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.309 51: 51: 51: Using 1 MPI thread 51: 51: Non-default thread affinity set, disabling internal thread affinity 51: 51: Using 2 OpenMP threads 51: 51: starting mdrun 'Water and methane' 51: 20 steps, 0.0 ps. 51: 51: 51: Received the remote INT/TERM signal, stopping within 50 steps 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: This run will generate roughly 0 Mb of data 51: 51: Writing final coordinates. 51: 51: Core t (s) Wall t (s) (%) 51: Time: 0.010 0.005 195.9 51: (ns/day) (hour/ns) 51: Performance: 723.112 0.033 51: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 51: log). 51: The current CPU can measure timings more accurately than the code in 51: gmxapi-test was configured to use. This might affect your simulation 51: speed as accurate timings are needed for load-balancing. 51: Please consider rebuilding gmxapi-test with the GMX_USE_RDTSCP=ON CMake option. 51: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.309 51: 51: 51: Using 1 MPI thread 51: 51: Non-default thread affinity set, disabling internal thread affinity 51: 51: Using 2 OpenMP threads 51: 51: starting mdrun 'Water and methane' 51: 20 steps, 0.0 ps. 51: 51: Writing final coordinates. 51: 51: Core t (s) Wall t (s) (%) 51: Time: 0.010 0.005 197.5 51: (ns/day) (hour/ns) 51: Performance: 712.164 0.034 51: [ OK ] GmxApiTest.RunnerReinitialize (666 ms) 51: [ RUN ] GmxApiTest.RunnerContinuedMD 51: Setting the LD random seed to -155585815 51: Generated 331705 of the 331705 non-bonded parameter combinations 51: Generating 1-4 interactions: fudge = 0.5 51: Generated 331705 of the 331705 1-4 parameter combinations 51: Excluding 2 bonded neighbours molecule type 'SOL' 51: Excluding 3 bonded neighbours molecule type 'methane' 51: 51: NOTE 1 [file spc_and_methane.top, line 33]: 51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 51: the time step of 2.0e-03 ps. 51: Maybe you forgot to change the constraints mdp option. 51: 51: Number of degrees of freedom in T-Coupling group System is 18.00 51: 51: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD_input.mdp]: 51: You are using a plain Coulomb cut-off, which might produce artifacts. 51: You might want to consider using PME electrostatics. 51: 51: 51: 51: There were 2 notes 51: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 51: log). 51: The current CPU can measure timings more accurately than the code in 51: gmxapi-test was configured to use. This might affect your simulation 51: speed as accurate timings are needed for load-balancing. 51: Please consider rebuilding gmxapi-test with the GMX_USE_RDTSCP=ON CMake option. 51: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.309 51: 51: 51: Using 1 MPI thread 51: 51: Non-default thread affinity set, disabling internal thread affinity 51: 51: Using 2 OpenMP threads 51: 51: starting mdrun 'Water and methane' 51: 10 steps, 0.0 ps. 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: This run will generate roughly 0 Mb of data 51: 51: Writing final coordinates. 51: 51: Core t (s) Wall t (s) (%) 51: Time: 0.107 0.054 199.6 51: (ns/day) (hour/ns) 51: Performance: 34.668 0.692 51: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 51: log). 51: The current CPU can measure timings more accurately than the code in 51: gmxapi-test was configured to use. This might affect your simulation 51: speed as accurate timings are needed for load-balancing. 51: Please consider rebuilding gmxapi-test with the GMX_USE_RDTSCP=ON CMake option. 51: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 51: 51: Overriding nsteps with value passed on the command line: 20 steps, 0.0391 ps 51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.309 51: 51: 51: Using 1 MPI thread 51: 51: Non-default thread affinity set, disabling internal thread affinity 51: 51: Using 2 OpenMP threads 51: 51: starting mdrun 'Water and methane' 51: 20 steps, 0.0 ps. 51: 51: Writing final coordinates. 51: 51: Core t (s) Wall t (s) (%) 51: Time: 0.011 0.006 195.1 51: (ns/day) (hour/ns) 51: Performance: 616.030 0.039 51: [ OK ] GmxApiTest.RunnerContinuedMD (606 ms) 51: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient 51: Setting the LD random seed to 800416987 51: Generated 331705 of the 331705 non-bonded parameter combinations 51: Generating 1-4 interactions: fudge = 0.5 51: Generated 331705 of the 331705 1-4 parameter combinations 51: Excluding 2 bonded neighbours molecule type 'SOL' 51: Excluding 3 bonded neighbours molecule type 'methane' 51: 51: NOTE 1 [file spc_and_methane.top, line 33]: 51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 51: the time step of 2.0e-03 ps. 51: Maybe you forgot to change the constraints mdp option. 51: 51: Number of degrees of freedom in T-Coupling group System is 18.00 51: 51: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 51: You are using a plain Coulomb cut-off, which might produce artifacts. 51: You might want to consider using PME electrostatics. 51: 51: 51: 51: There were 2 notes 51: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 51: log). 51: The current CPU can measure timings more accurately than the code in 51: gmxapi-test was configured to use. This might affect your simulation 51: speed as accurate timings are needed for load-balancing. 51: Please consider rebuilding gmxapi-test with the GMX_USE_RDTSCP=ON CMake option. 51: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 51: Changing nstlist from 10 to 1, rlist from 1.041 to 1 51: 51: 51: Using 1 MPI thread 51: 51: Non-default thread affinity set, disabling internal thread affinity 51: 51: Using 2 OpenMP threads 51: 51: starting mdrun 'Water and methane' 51: 1 steps, 0.0 ps. 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: This run will generate roughly 0 Mb of data 51: 51: Writing final coordinates. 51: 51: Core t (s) Wall t (s) (%) 51: Time: 0.386 0.193 199.9 51: (ns/day) (hour/ns) 51: Performance: 1.749 13.722 51: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 51: log). 51: The current CPU can measure timings more accurately than the code in 51: gmxapi-test was configured to use. This might affect your simulation 51: speed as accurate timings are needed for load-balancing. 51: Please consider rebuilding gmxapi-test with the GMX_USE_RDTSCP=ON CMake option. 51: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 51: 51: Overriding nsteps with value passed on the command line: 2 steps, 0.00391 ps 51: Changing nstlist from 10 to 1, rlist from 1.041 to 1 51: 51: 51: Using 1 MPI thread 51: 51: Non-default thread affinity set, disabling internal thread affinity 51: 51: Using 2 OpenMP threads 51: 51: starting mdrun 'Water and methane' 51: 2 steps, 0.0 ps. 51: 51: Core t (s) Wall t (s) (%) 51: Time: 0.007 0.004 193.6 51: (ns/day) (hour/ns) 51: Performance: 94.555 0.254 51: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (821 ms) 51: [----------] 8 tests from GmxApiTest (4608 ms total) 51: 51: [----------] 1 test from GmxApiBasicTest 51: [ RUN ] GmxApiBasicTest.Status 51: [ OK ] GmxApiBasicTest.Status (0 ms) 51: [----------] 1 test from GmxApiBasicTest (0 ms total) 51: 51: [----------] Global test environment tear-down 51: [==========] 9 tests from 2 test cases ran. (4608 ms total) 51: [ PASSED ] 9 tests. 51/54 Test #51: GmxapiExternalInterfaceTests ........ Passed 4.63 sec test 52 Start 52: GmxapiMpiTests 52: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/gmxapi-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/GmxapiMpiTests.xml" 52: Test timeout computed to be: 600 52: [==========] Running 9 tests from 2 test cases. 52: [----------] Global test environment set-up. 52: [----------] 8 tests from GmxApiTest 52: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD 52: Setting the LD random seed to -71176441 52: Generated 331705 of the 331705 non-bonded parameter combinations 52: Generating 1-4 interactions: fudge = 0.5 52: Generated 331705 of the 331705 1-4 parameter combinations 52: Excluding 2 bonded neighbours molecule type 'SOL' 52: Excluding 3 bonded neighbours molecule type 'methane' 52: 52: NOTE 1 [file spc_and_methane.top, line 33]: 52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 52: the time step of 2.0e-03 ps. 52: Maybe you forgot to change the constraints mdp option. 52: 52: Number of degrees of freedom in T-Coupling group System is 18.00 52: 52: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 52: You are using a plain Coulomb cut-off, which might produce artifacts. 52: You might want to consider using PME electrostatics. 52: 52: 52: 52: There were 2 notes 52: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 52: log). 52: The current CPU can measure timings more accurately than the code in 52: gmxapi-mpi-test was configured to use. This might affect your simulation 52: speed as accurate timings are needed for load-balancing. 52: Please consider rebuilding gmxapi-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 52: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.309 52: 52: 52: Using 1 MPI thread 52: 52: Non-default thread affinity set, disabling internal thread affinity 52: 52: Using 2 OpenMP threads 52: 52: starting mdrun 'Water and methane' 52: 2 steps, 0.0 ps. 52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 52: Note that mdrun will redetermine rlist based on the actual pair-list setup 52: This run will generate roughly 0 Mb of data 52: 52: Writing final coordinates. 52: 52: Core t (s) Wall t (s) (%) 52: Time: 0.007 0.004 194.5 52: (ns/day) (hour/ns) 52: Performance: 143.036 0.168 52: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (640 ms) 52: [ RUN ] GmxApiTest.SystemConstruction 52: Setting the LD random seed to -137897353 52: Generated 331705 of the 331705 non-bonded parameter combinations 52: Generating 1-4 interactions: fudge = 0.5 52: Generated 331705 of the 331705 1-4 parameter combinations 52: Excluding 2 bonded neighbours molecule type 'SOL' 52: Excluding 3 bonded neighbours molecule type 'methane' 52: 52: NOTE 1 [file spc_and_methane.top, line 33]: 52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 52: the time step of 2.0e-03 ps. 52: Maybe you forgot to change the constraints mdp option. 52: 52: Number of degrees of freedom in T-Coupling group System is 18.00 52: 52: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 52: You are using a plain Coulomb cut-off, which might produce artifacts. 52: You might want to consider using PME electrostatics. 52: 52: 52: 52: There were 2 notes 52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 52: Note that mdrun will redetermine rlist based on the actual pair-list setup 52: This run will generate roughly 0 Mb of data 52: [ OK ] GmxApiTest.SystemConstruction (630 ms) 52: [ RUN ] GmxApiTest.SaneVersionComparisons 52: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) 52: [ RUN ] GmxApiTest.VersionNamed0_1_Features 52: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) 52: [ RUN ] GmxApiTest.RunnerBasicMD 52: Setting the LD random seed to -8560707 52: Generated 331705 of the 331705 non-bonded parameter combinations 52: Generating 1-4 interactions: fudge = 0.5 52: Generated 331705 of the 331705 1-4 parameter combinations 52: Excluding 2 bonded neighbours molecule type 'SOL' 52: Excluding 3 bonded neighbours molecule type 'methane' 52: 52: NOTE 1 [file spc_and_methane.top, line 33]: 52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 52: the time step of 2.0e-03 ps. 52: Maybe you forgot to change the constraints mdp option. 52: 52: Number of degrees of freedom in T-Coupling group System is 18.00 52: 52: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 52: You are using a plain Coulomb cut-off, which might produce artifacts. 52: You might want to consider using PME electrostatics. 52: 52: 52: 52: There were 2 notes 52: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 52: log). 52: The current CPU can measure timings more accurately than the code in 52: gmxapi-mpi-test was configured to use. This might affect your simulation 52: speed as accurate timings are needed for load-balancing. 52: Please consider rebuilding gmxapi-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 52: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.309 52: 52: 52: Using 1 MPI thread 52: 52: Non-default thread affinity set, disabling internal thread affinity 52: 52: Using 2 OpenMP threads 52: 52: starting mdrun 'Water and methane' 52: 2 steps, 0.0 ps. 52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 52: Note that mdrun will redetermine rlist based on the actual pair-list setup 52: This run will generate roughly 0 Mb of data 52: 52: Writing final coordinates. 52: 52: Core t (s) Wall t (s) (%) 52: Time: 0.102 0.051 199.7 52: (ns/day) (hour/ns) 52: Performance: 9.929 2.417 52: [ OK ] GmxApiTest.RunnerBasicMD (624 ms) 52: [ RUN ] GmxApiTest.RunnerReinitialize 52: Setting the LD random seed to -271060065 52: Generated 331705 of the 331705 non-bonded parameter combinations 52: Generating 1-4 interactions: fudge = 0.5 52: Generated 331705 of the 331705 1-4 parameter combinations 52: Excluding 2 bonded neighbours molecule type 'SOL' 52: Excluding 3 bonded neighbours molecule type 'methane' 52: 52: NOTE 1 [file spc_and_methane.top, line 33]: 52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 52: the time step of 2.0e-03 ps. 52: Maybe you forgot to change the constraints mdp option. 52: 52: Number of degrees of freedom in T-Coupling group System is 18.00 52: 52: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 52: You are using a plain Coulomb cut-off, which might produce artifacts. 52: You might want to consider using PME electrostatics. 52: 52: 52: 52: There were 2 notes 52: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 52: log). 52: The current CPU can measure timings more accurately than the code in 52: gmxapi-mpi-test was configured to use. This might affect your simulation 52: speed as accurate timings are needed for load-balancing. 52: Please consider rebuilding gmxapi-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 52: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.309 52: 52: 52: Using 1 MPI thread 52: 52: Non-default thread affinity set, disabling internal thread affinity 52: 52: Using 2 OpenMP threads 52: 52: starting mdrun 'Water and methane' 52: 20 steps, 0.0 ps. 52: 52: 52: Received the remote INT/TERM signal, stopping within 50 steps 52: 52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 52: Note that mdrun will redetermine rlist based on the actual pair-list setup 52: This run will generate roughly 0 Mb of data 52: 52: Writing final coordinates. 52: 52: Core t (s) Wall t (s) (%) 52: Time: 0.010 0.005 197.1 52: (ns/day) (hour/ns) 52: Performance: 681.627 0.035 52: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 52: log). 52: The current CPU can measure timings more accurately than the code in 52: gmxapi-mpi-test was configured to use. This might affect your simulation 52: speed as accurate timings are needed for load-balancing. 52: Please consider rebuilding gmxapi-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 52: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.309 52: 52: 52: Using 1 MPI thread 52: 52: Non-default thread affinity set, disabling internal thread affinity 52: 52: Using 2 OpenMP threads 52: 52: starting mdrun 'Water and methane' 52: 20 steps, 0.0 ps. 52: 52: Writing final coordinates. 52: 52: Core t (s) Wall t (s) (%) 52: Time: 0.008 0.004 196.8 52: (ns/day) (hour/ns) 52: Performance: 906.702 0.026 52: [ OK ] GmxApiTest.RunnerReinitialize (584 ms) 52: [ RUN ] GmxApiTest.RunnerContinuedMD 52: Setting the LD random seed to 534543999 52: Generated 331705 of the 331705 non-bonded parameter combinations 52: Generating 1-4 interactions: fudge = 0.5 52: Generated 331705 of the 331705 1-4 parameter combinations 52: Excluding 2 bonded neighbours molecule type 'SOL' 52: Excluding 3 bonded neighbours molecule type 'methane' 52: 52: NOTE 1 [file spc_and_methane.top, line 33]: 52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 52: the time step of 2.0e-03 ps. 52: Maybe you forgot to change the constraints mdp option. 52: 52: Number of degrees of freedom in T-Coupling group System is 18.00 52: 52: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD_input.mdp]: 52: You are using a plain Coulomb cut-off, which might produce artifacts. 52: You might want to consider using PME electrostatics. 52: 52: 52: 52: There were 2 notes 52: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 52: log). 52: The current CPU can measure timings more accurately than the code in 52: gmxapi-mpi-test was configured to use. This might affect your simulation 52: speed as accurate timings are needed for load-balancing. 52: Please consider rebuilding gmxapi-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 52: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.309 52: 52: 52: Using 1 MPI thread 52: 52: Non-default thread affinity set, disabling internal thread affinity 52: 52: Using 2 OpenMP threads 52: 52: starting mdrun 'Water and methane' 52: 10 steps, 0.0 ps. 52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 52: Note that mdrun will redetermine rlist based on the actual pair-list setup 52: This run will generate roughly 0 Mb of data 52: 52: Writing final coordinates. 52: 52: Core t (s) Wall t (s) (%) 52: Time: 0.011 0.006 195.8 52: (ns/day) (hour/ns) 52: Performance: 326.457 0.074 52: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 52: log). 52: The current CPU can measure timings more accurately than the code in 52: gmxapi-mpi-test was configured to use. This might affect your simulation 52: speed as accurate timings are needed for load-balancing. 52: Please consider rebuilding gmxapi-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 52: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 52: 52: Overriding nsteps with value passed on the command line: 20 steps, 0.0391 ps 52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.309 52: 52: 52: Using 1 MPI thread 52: 52: Non-default thread affinity set, disabling internal thread affinity 52: 52: Using 2 OpenMP threads 52: 52: starting mdrun 'Water and methane' 52: 20 steps, 0.0 ps. 52: 52: Writing final coordinates. 52: 52: Core t (s) Wall t (s) (%) 52: Time: 0.010 0.005 195.7 52: (ns/day) (hour/ns) 52: Performance: 688.255 0.035 52: [ OK ] GmxApiTest.RunnerContinuedMD (677 ms) 52: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient 52: Setting the LD random seed to -19071057 52: Generated 331705 of the 331705 non-bonded parameter combinations 52: Generating 1-4 interactions: fudge = 0.5 52: Generated 331705 of the 331705 1-4 parameter combinations 52: Excluding 2 bonded neighbours molecule type 'SOL' 52: Excluding 3 bonded neighbours molecule type 'methane' 52: 52: NOTE 1 [file spc_and_methane.top, line 33]: 52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 52: the time step of 2.0e-03 ps. 52: Maybe you forgot to change the constraints mdp option. 52: 52: Number of degrees of freedom in T-Coupling group System is 18.00 52: 52: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 52: You are using a plain Coulomb cut-off, which might produce artifacts. 52: You might want to consider using PME electrostatics. 52: 52: 52: 52: There were 2 notes 52: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 52: log). 52: The current CPU can measure timings more accurately than the code in 52: gmxapi-mpi-test was configured to use. This might affect your simulation 52: speed as accurate timings are needed for load-balancing. 52: Please consider rebuilding gmxapi-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 52: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 52: Changing nstlist from 10 to 1, rlist from 1.041 to 1 52: 52: 52: Using 1 MPI thread 52: 52: Non-default thread affinity set, disabling internal thread affinity 52: 52: Using 2 OpenMP threads 52: 52: starting mdrun 'Water and methane' 52: 1 steps, 0.0 ps. 52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 52: Note that mdrun will redetermine rlist based on the actual pair-list setup 52: This run will generate roughly 0 Mb of data 52: 52: Writing final coordinates. 52: 52: Core t (s) Wall t (s) (%) 52: Time: 0.006 0.003 195.6 52: (ns/day) (hour/ns) 52: Performance: 116.990 0.205 52: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 52: log). 52: The current CPU can measure timings more accurately than the code in 52: gmxapi-mpi-test was configured to use. This might affect your simulation 52: speed as accurate timings are needed for load-balancing. 52: Please consider rebuilding gmxapi-mpi-test with the GMX_USE_RDTSCP=ON CMake option. 52: Reading file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.6-Debian-2020.6-2 (double precision) 52: 52: Overriding nsteps with value passed on the command line: 2 steps, 0.00391 ps 52: Changing nstlist from 10 to 1, rlist from 1.041 to 1 52: 52: 52: Using 1 MPI thread 52: 52: Non-default thread affinity set, disabling internal thread affinity 52: 52: Using 2 OpenMP threads 52: 52: starting mdrun 'Water and methane' 52: 2 steps, 0.0 ps. 52: 52: Core t (s) Wall t (s) (%) 52: Time: 0.006 0.003 196.2 52: (ns/day) (hour/ns) 52: Performance: 118.024 0.203 52: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (704 ms) 52: [----------] 8 tests from GmxApiTest (3861 ms total) 52: 52: [----------] 1 test from GmxApiBasicTest 52: [ RUN ] GmxApiBasicTest.Status 52: [ OK ] GmxApiBasicTest.Status (0 ms) 52: [----------] 1 test from GmxApiBasicTest (0 ms total) 52: 52: [----------] Global test environment tear-down 52: [==========] 9 tests from 2 test cases ran. (3861 ms total) 52: [ PASSED ] 9 tests. 52/54 Test #52: GmxapiMpiTests ...................... Passed 3.89 sec test 53 Start 53: GmxapiInternalInterfaceTests 53: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/GmxapiInternalInterfaceTests.xml" 53: Test timeout computed to be: 600 53: [==========] Running 2 tests from 1 test case. 53: [----------] Global test environment set-up. 53: [----------] 2 tests from GmxApiTest 53: [ RUN ] GmxApiTest.BuildApiWorkflowImpl 53: Setting the LD random seed to 1068350231 53: Generated 331705 of the 331705 non-bonded parameter combinations 53: Generating 1-4 interactions: fudge = 0.5 53: Generated 331705 of the 331705 1-4 parameter combinations 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: Excluding 3 bonded neighbours molecule type 'methane' 53: 53: NOTE 1 [file spc_and_methane.top, line 33]: 53: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 53: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 53: the time step of 2.0e-03 ps. 53: Maybe you forgot to change the constraints mdp option. 53: 53: Number of degrees of freedom in T-Coupling group System is 18.00 53: 53: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 2 notes 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 53: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 53: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: This run will generate roughly 0 Mb of data 53: [ OK ] GmxApiTest.BuildApiWorkflowImpl (668 ms) 53: [ RUN ] GmxApiTest.CreateApiWorkflow 53: Setting the LD random seed to -1222246531 53: Generated 331705 of the 331705 non-bonded parameter combinations 53: Generating 1-4 interactions: fudge = 0.5 53: Generated 331705 of the 331705 1-4 parameter combinations 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: Excluding 3 bonded neighbours molecule type 'methane' 53: 53: NOTE 1 [file spc_and_methane.top, line 33]: 53: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 53: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 53: the time step of 2.0e-03 ps. 53: Maybe you forgot to change the constraints mdp option. 53: 53: Number of degrees of freedom in T-Coupling group System is 18.00 53: 53: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 2 notes 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 53: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 53: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: This run will generate roughly 0 Mb of data 53: [ OK ] GmxApiTest.CreateApiWorkflow (536 ms) 53: [----------] 2 tests from GmxApiTest (1204 ms total) 53: 53: [----------] Global test environment tear-down 53: [==========] 2 tests from 1 test case ran. (1205 ms total) 53: [ PASSED ] 2 tests. 53/54 Test #53: GmxapiInternalInterfaceTests ........ Passed 1.22 sec test 54 Start 54: GmxapiInternalsMpiTests 54: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/bin/workflow-details-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/Testing/Temporary/GmxapiInternalsMpiTests.xml" 54: Test timeout computed to be: 600 54: [==========] Running 2 tests from 1 test case. 54: [----------] Global test environment set-up. 54: [----------] 2 tests from GmxApiTest 54: [ RUN ] GmxApiTest.BuildApiWorkflowImpl 54: Setting the LD random seed to -408945681 54: Generated 331705 of the 331705 non-bonded parameter combinations 54: Generating 1-4 interactions: fudge = 0.5 54: Generated 331705 of the 331705 1-4 parameter combinations 54: Excluding 2 bonded neighbours molecule type 'SOL' 54: Excluding 3 bonded neighbours molecule type 'methane' 54: 54: NOTE 1 [file spc_and_methane.top, line 33]: 54: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 54: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 54: the time step of 2.0e-03 ps. 54: Maybe you forgot to change the constraints mdp option. 54: 54: Number of degrees of freedom in T-Coupling group System is 18.00 54: 54: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 54: You are using a plain Coulomb cut-off, which might produce artifacts. 54: You might want to consider using PME electrostatics. 54: 54: 54: 54: There were 2 notes 54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 54: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 54: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 54: Note that mdrun will redetermine rlist based on the actual pair-list setup 54: This run will generate roughly 0 Mb of data 54: [ OK ] GmxApiTest.BuildApiWorkflowImpl (620 ms) 54: [ RUN ] GmxApiTest.CreateApiWorkflow 54: Setting the LD random seed to -37750004 54: Generated 331705 of the 331705 non-bonded parameter combinations 54: Generating 1-4 interactions: fudge = 0.5 54: Generated 331705 of the 331705 1-4 parameter combinations 54: Excluding 2 bonded neighbours molecule type 'SOL' 54: Excluding 3 bonded neighbours molecule type 'methane' 54: 54: NOTE 1 [file spc_and_methane.top, line 33]: 54: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 54: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 54: the time step of 2.0e-03 ps. 54: Maybe you forgot to change the constraints mdp option. 54: 54: Number of degrees of freedom in T-Coupling group System is 18.00 54: 54: NOTE 2 [file /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 54: You are using a plain Coulomb cut-off, which might produce artifacts. 54: You might want to consider using PME electrostatics. 54: 54: 54: 54: There were 2 notes 54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 54: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 54: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm 54: Note that mdrun will redetermine rlist based on the actual pair-list setup 54: This run will generate roughly 0 Mb of data 54: [ OK ] GmxApiTest.CreateApiWorkflow (632 ms) 54: [----------] 2 tests from GmxApiTest (1253 ms total) 54: 54: [----------] Global test environment tear-down 54: [==========] 2 tests from 1 test case ran. (1253 ms total) 54: [ PASSED ] 2 tests. 54/54 Test #54: GmxapiInternalsMpiTests ............. Passed 1.31 sec 100% tests passed, 0 tests failed out of 54 Label Time Summary: GTest = 149.66 sec*proc (54 tests) IntegrationTest = 48.56 sec*proc (12 tests) MpiTest = 82.56 sec*proc (8 tests) SlowTest = 71.91 sec*proc (2 tests) UnitTest = 29.19 sec*proc (40 tests) Total Test time (real) = 149.78 sec touch build-basic dh_testdir /usr/bin/make -j4 -C build/mpich make[1]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/cmake -S/build/gromacs-5atmZb/gromacs-2020.6 -B/build/gromacs-5atmZb/gromacs-2020.6/build/mpich --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/CMakeFiles /build/gromacs-5atmZb/gromacs-2020.6/build/mpich//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/selection /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/CMakeFiles/release-version-info.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color= Scanning dependencies of target release-version-info make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.6-Debian-2020.6-2 -D PROJECT_SOURCE_DIR=/build/gromacs-5atmZb/gromacs-2020.6 -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2020.6-2 -P /build/gromacs-5atmZb/gromacs-2020.6/cmake/gmxGenerateVersionInfoRelease.cmake Scanning dependencies of target scanner Scanning dependencies of target lmfit_objlib make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/selection && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/parser.cpp make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++14 -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit/lmmin.cpp Scanning dependencies of target thread_mpi make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/errhandler.cpp make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 0%] Built target release-version-info cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/tmpi_malloc.cpp /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/atomic.cpp Scanning dependencies of target tng_io_obj make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/bwlzh.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/lock.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/pthreads.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/system_error.cpp make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 1%] Built target thread_mpi /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/linearalgebra /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= Scanning dependencies of target linearalgebra make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra/eigensolver.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/bwt.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/coder.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra/gmx_arpack.cpp make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 1%] Built target lmfit_objlib /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color= Scanning dependencies of target modularsimulator make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/checkpointhelper.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/dict.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/fixpoint.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/huffman.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/huffmem.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/compositesimulatorelement.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/lz77.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/merge_sort.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/mtf.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/computeglobalselement.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/rle.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/tng_compress.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/selection && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/scanner.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/constraintelement.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra/matrix.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/vals16.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/warnmalloc.c make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/widemuldiv.c [ 1%] Built target scanner /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun_objlib make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/mdrun.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/xtc2.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra/nrjac.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/domdechelper.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra/sparsematrix.cpp make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 1%] Built target linearalgebra cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/nonbonded_bench.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/xtc3.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/lib/tng_io.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/energyelement.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/energyelement.cpp make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 2%] Built target mdrun_objlib cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/lib/md5.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/forceelement.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/freeenergyperturbationelement.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/modularsimulator.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/propagator.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/shellfcelement.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/shellfcelement.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 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/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/statepropagatordata.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/topologyholder.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/trajectoryelement.cpp make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 5%] Built target tng_io_obj cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/vrescalethermostat.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/vrescalethermostat.cpp make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 8%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/VersionInfo.cmake -D VERSION_CMAKEIN=/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/gromacs-5atmZb/gromacs-2020.6/cmake/gmxConfigureVersionInfo.cmake cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= Scanning dependencies of target libgromacs make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/alignedallocator.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H 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/build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/cstringutil.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem 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/build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/gridset.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernel_common.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem 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/build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_reference/kernel_ref.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_prune.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops 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CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/nbnxm_geometry.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/nbnxm_setup.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/pairlist.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/pairlist_tuning.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/pairlistparams.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/pairlistset.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/pairsearch.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/prunekerneldispatch.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/cmdlinehelpcontext.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/cmdlinehelpmodule.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/cmdlinehelpwriter.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/cmdlineinit.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/cmdlinemodule.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/cmdlinemodulemanager.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/cmdlineoptionsmodule.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/cmdlineparser.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/cmdlineprogramcontext.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/filenm.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/pargs.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/shellcompletions.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/viewit.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/domdec/atomdistribution.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/domdec/box.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/domdec/cellsizes.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/domdec/collect.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/domdec/distribute.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/domdec/dlb.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/domdec/dlbtiming.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/domdec/domdec.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/domdec/domdec_constraints.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/domdec/domdec_network.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/domdec/domdec_setup.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/domdec/domdec_specatomcomm.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/domdec/domdec_topology.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/domdec/domdec_vsite.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c 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/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/domdec/ga2la.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/domdec/gpuhaloexchange_impl.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/domdec/localatomset.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/domdec/localatomsetdata.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/domdec/localatomsetmanager.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/domdec/mdsetup.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c 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/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/domdec/redistribute.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/domdec/utility.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/3dtransforms.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/coordinatetransformation.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -c 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/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/gausstransform.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/invertmatrix.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/units.cpp.o -c 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/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/veccompare.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c 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/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdtypes/iforceprovider.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-class-memaccess -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c 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/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdtypes/md_enums.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdtypes/observableshistory.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c 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/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/onlinehelp/helptopic.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/onlinehelp/helpwritercontext.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/onlinehelp/rstparser.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/pbcutil/boxutilities.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/pbcutil/mshift.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/pbcutil/pbc.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/pbcutil/pbc_simd.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/pbcutil/pbcenums.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/pbcutil/pbcmethods.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/pbcutil/rmpbc.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c 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/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/random/tabulatednormaldistribution.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/tables/cubicsplinetable.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/tables/forcetable.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/tables/quadraticsplinetable.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c 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/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/topology/topsort.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/swap/swapcoords.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/essentialdynamics/edsam.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/pulling/output.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/pulling/pull.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/pulling/pull_rotation.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/pulling/pullutil.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/awh.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/awh/awh.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/bias.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/awh/bias.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && 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-I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/awh/biasstate.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src 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/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/lincs.cpp /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/forcerec.cpp: In function ‘void __static_initialization_and_destruction_0(int, int)’: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/forcerec.cpp:103:16: warning: ignoring return value of ‘char* getenv(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 103 | (getenv("GMX_GPU_PME_PP_COMMS") != nullptr) && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/md_support.cpp cd 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/usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/rbin.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/resethandler.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/rf_util.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src 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/build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/pme.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem 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/build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/pme_only.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/pme_pp.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/pme_redistribute.cpp /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/pme_only.cpp: In function ‘void __static_initialization_and_destruction_0(int, int)’: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/pme_only.cpp:104:16: warning: ignoring return value of ‘char* getenv(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 104 | (getenv("GMX_GPU_PME_PP_COMMS") != nullptr) && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp 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-I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdrun/minimize.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdrun/replicaexchange.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdrun/rerun.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem 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CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o 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/usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [100%] Built target mdrun make[2]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/cmake -E cmake_progress_start /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/CMakeFiles 0 make[1]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -j4 -C build/mpich-dp make[1]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' /usr/bin/cmake -S/build/gromacs-5atmZb/gromacs-2020.6 -B/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/CMakeFiles /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake --color= Scanning dependencies of target release-version-info make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs 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PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.6-Debian-2020.6-2 -D PROJECT_SOURCE_DIR=/build/gromacs-5atmZb/gromacs-2020.6 -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2020.6-2 -P /build/gromacs-5atmZb/gromacs-2020.6/cmake/gmxGenerateVersionInfoRelease.cmake Scanning dependencies of target lmfit_objlib make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++14 -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit/lmmin.cpp Scanning dependencies of target thread_mpi make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/errhandler.cpp make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' Scanning dependencies of target scanner make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build [ 0%] Built target release-version-info /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs/selection && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/parser.cpp make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= Scanning dependencies of target tng_io_obj make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/bwlzh.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/tmpi_malloc.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/atomic.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/lock.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/pthreads.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/system_error.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/bwt.c make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' [ 1%] Built target thread_mpi /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs/linearalgebra /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= Scanning dependencies of target linearalgebra make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra/eigensolver.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/coder.c make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' [ 1%] Built target lmfit_objlib /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs/modularsimulator /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color= Scanning dependencies of target modularsimulator make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/checkpointhelper.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/dict.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/fixpoint.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/huffman.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/huffmem.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/lz77.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/compositesimulatorelement.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/merge_sort.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/mtf.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/computeglobalselement.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/rle.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/tng_compress.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs/selection && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/scanner.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/constraintelement.cpp make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' [ 1%] Built target scanner /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun_objlib make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/mdrun.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/vals16.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/warnmalloc.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/widemuldiv.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra/matrix.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/xtc2.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra/nrjac.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/domdechelper.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/nonbonded_bench.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/xtc3.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/energyelement.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/energyelement.cpp make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' [ 1%] Built target linearalgebra cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/forceelement.cpp make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' [ 2%] Built target mdrun_objlib cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/freeenergyperturbationelement.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. 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/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/lib/tng_io.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src 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'/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' [ 5%] Built target tng_io_obj make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' [ 8%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/gromacs-5atmZb/gromacs-2020.6/cmake/gmxConfigureVersionInfo.cmake cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= Scanning dependencies of target libgromacs make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem 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-I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_prune.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. 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/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/lincs.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/md_support.cpp /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/forcerec.cpp: In function ‘void __static_initialization_and_destruction_0(int, int)’: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/forcerec.cpp:103:16: warning: ignoring return value of ‘char* getenv(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 103 | (getenv("GMX_GPU_PME_PP_COMMS") != nullptr) && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/mdatoms.cpp 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/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/long_range_correction.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/pme.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/pme_gather.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/pme_grid.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/pme_load_balancing.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/pme_only.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/pme_pp.cpp /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/pme_only.cpp: In function ‘void __static_initialization_and_destruction_0(int, int)’: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/pme_only.cpp:104:16: warning: ignoring return value of ‘char* getenv(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 104 | (getenv("GMX_GPU_PME_PP_COMMS") != nullptr) && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include 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'/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/linearalgebra /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color= [ 1%] Built target release-version-info /usr/bin/make -f src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build.make src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/depend make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' make[4]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/external/googletest/googlemock/gtest /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/DependInfo.cmake --color= [ 1%] Built target linearalgebra [ 3%] Built target tng_io_obj make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 5%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend Scanning dependencies of target gtest make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build.make src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/external/googletest/googlemock/gtest && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wshadow -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=c++14 -o CMakeFiles/gtest.dir/src/gtest-all.cc.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/src/gtest-all.cc make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 72%] Built target libgromacs cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/external/googletest/googlemock/gtest && /usr/bin/cmake -P CMakeFiles/gtest.dir/cmake_clean_target.cmake cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/external/googletest/googlemock/gtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../../lib/libgtest.a CMakeFiles/gtest.dir/src/gtest-all.cc.o /usr/bin/ranlib ../../../../../lib/libgtest.a make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 72%] Built target gtest /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/external/googletest/googlemock /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/external/googletest/googlemock/CMakeFiles/gmock.dir/DependInfo.cmake --color= Scanning dependencies of target gmock make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/external/googletest/googlemock && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_CAN_STREAM_RESULTS=0 -D_GNU_SOURCE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wshadow -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated-copy -std=c++14 -o CMakeFiles/gmock.dir/src/gmock-all.cc.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/src/gmock-all.cc cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/external/googletest/googlemock && /usr/bin/cmake -P CMakeFiles/gmock.dir/cmake_clean_target.cmake cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libgmock.a CMakeFiles/gmock.dir/src/gmock-all.cc.o /usr/bin/ranlib ../../../../lib/libgmock.a make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 73%] Built target gmock /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/testutils /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/testutils /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/testutils/CMakeFiles/testutils.dir/DependInfo.cmake --color= Scanning dependencies of target testutils make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/cmdlinetest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/cmdlinetest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/conftest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/conftest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/filematchers.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/filematchers.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/interactivetest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/interactivetest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/loggertest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/loggertest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/mpi_printer.cpp.o -c 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CMakeFiles/testutils.dir/textblockmatchers.cpp.o CMakeFiles/testutils.dir/tprfilegenerator.cpp.o CMakeFiles/testutils.dir/xvgtest.cpp.o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o /usr/bin/ranlib ../../lib/libtestutils.a make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 76%] Built target testutils /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/depend /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/depend /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/testutils/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/testutils/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/testutils/tests/CMakeFiles/testutils-test.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/selection/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake --color= Scanning dependencies of target testutils-mpi-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build Scanning dependencies of target utility-mpi-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/tests/mpitest.cpp make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/physicalnodecommunicator_mpi.cpp Scanning dependencies of target testutils-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/interactivetest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/tests/interactivetest.cpp Scanning dependencies of target selection-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/selection/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/tests/indexutil.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../lib/libgtest.a -lpthread cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/tests/refdata_tests.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 77%] Built target utility-mpi-test [ 77%] Built target testutils-mpi-test /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/depend cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/selection/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/tests/nbsearch.cpp make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake --color= Scanning dependencies of target utility-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/alignedallocator.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/arrayref.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/selection/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/tests/poscalc.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/tests/testasserts_tests.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/bitmask32.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/selection/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/tests/selectioncollection.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/tests/xvgtest_tests.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/selection/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/tests/selectionoption.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-test.dir/interactivetest.cpp.o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../lib/libgtest.a -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 77%] Built target testutils-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/selection/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/tests/toputils.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/bitmask64.cpp /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdlib-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/calc_verletbuf.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/constr.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/constrtestdata.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/selection/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/selection-test.dir/indexutil.cpp.o CMakeFiles/selection-test.dir/nbsearch.cpp.o CMakeFiles/selection-test.dir/poscalc.cpp.o CMakeFiles/selection-test.dir/selectioncollection.cpp.o CMakeFiles/selection-test.dir/selectionoption.cpp.o CMakeFiles/selection-test.dir/toputils.cpp.o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/applied_forces/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/applied_forces/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake --color= Scanning dependencies of target applied_forces-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/applied_forces/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfitting.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/applied_forces/tests/densityfitting.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 78%] Built target selection-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/bitmask128.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/constrtestrunners.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/applied_forces/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfittingoptions.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/applied_forces/tests/densityfittingoptions.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/ebin.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/energyoutput.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/applied_forces/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/applied_forces/tests/densityfittingamplitudelookup.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/applied_forces/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/applied_forces/tests/electricfield.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/applied_forces/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/expanded.cpp /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/onlinehelp/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/onlinehelp/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color= Scanning dependencies of target onlinehelp-test-shared make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/onlinehelp/tests/mock_helptopic.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/cstringutil.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/applied_forces-test.dir/densityfitting.cpp.o CMakeFiles/applied_forces-test.dir/densityfittingoptions.cpp.o CMakeFiles/applied_forces-test.dir/densityfittingamplitudelookup.cpp.o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 78%] Built target applied_forces-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/defaultinitializationallocator.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/leapfrog.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/enumerationhelpers.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o /usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 78%] Built target onlinehelp-test-shared cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/fixedcapacityvector.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/leapfrogtestdata.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/inmemoryserializer.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/keyvaluetreeserializer.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/keyvaluetreetransform.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/settle.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/settletestdata.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/logger.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/logger.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/settletestrunners.cpp /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/domdec/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/domdec/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color= Scanning dependencies of target domdec-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/domdec/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/domdec/tests/hashedmap.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/shake.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/mutex.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/simulationsignal.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/domdec/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/domdec/tests/localatomsetmanager.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/path.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/path.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/updategroups.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/domdec/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/domdec-test.dir/hashedmap.cpp.o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/updategroupscog.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/physicalnodecommunicator.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 78%] Built target domdec-test /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/ewald/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color= Scanning dependencies of target ewald-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/tests/pmebsplinetest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/stringutil.cpp /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fft/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/fft/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color= Scanning dependencies of target fft-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/fft/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/fft/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fft-test.dir/fft.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fft/tests/fft.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/constr.cpp.o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o CMakeFiles/mdlib-test.dir/ebin.cpp.o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o CMakeFiles/mdlib-test.dir/expanded.cpp.o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o CMakeFiles/mdlib-test.dir/settle.cpp.o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o CMakeFiles/mdlib-test.dir/shake.cpp.o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o CMakeFiles/mdlib-test.dir/updategroups.cpp.o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 80%] Built target mdlib-test /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gpu_utils/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/gpu_utils/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color= Scanning dependencies of target gpu_utils-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/gputest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gpu_utils/tests/gputest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/tests/pmegathertest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/fft/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/fft/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gpu_utils/tests/clfftinitializer.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fft-test.dir/fft.cpp.o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 80%] Built target fft-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gpu_utils/tests/hostallocator.cpp /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/hardware/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/hardware/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color= Scanning dependencies of target hardware-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/hardware/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/hardware/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/hardware/tests/hardwaretopology.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/textreader.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/hardware/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/hardware/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 80%] Built target hardware-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/textwriter.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/tests/pmesolvetest.cpp /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/math/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color= Scanning dependencies of target math-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/arrayrefwithpadding.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/typetraits.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-test.dir/alignedallocator.cpp.o CMakeFiles/utility-test.dir/arrayref.cpp.o CMakeFiles/utility-test.dir/bitmask32.cpp.o CMakeFiles/utility-test.dir/bitmask64.cpp.o CMakeFiles/utility-test.dir/bitmask128.cpp.o CMakeFiles/utility-test.dir/cstringutil.cpp.o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/stringutil.cpp.o CMakeFiles/utility-test.dir/textreader.cpp.o CMakeFiles/utility-test.dir/textwriter.cpp.o CMakeFiles/utility-test.dir/typetraits.cpp.o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 83%] Built target utility-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdrunutility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-test-shared make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/coordinatetransformation.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/tests/pmesplinespreadtest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o /usr/bin/ranlib ../../../../lib/libmdrunutility-test-shared.a make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 84%] Built target mdrunutility-test-shared cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/tests/pmetestcommon.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gpu_utils/tests/devicetransfers.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gpu_utils-test.dir/gputest.cpp.o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/densityfit.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/densityfit.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 84%] Built target gpu_utils-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/tests/testhardwarecontexts.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/dofit.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/dofit.cpp /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdspan/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdspan/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdspan-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdspan/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdspan/tests/accessor_policy.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/exponentialmovingaverage.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdspan/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/extents.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdspan/tests/extents.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 85%] Built target ewald-test /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/onlinehelp/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/onlinehelp/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color= Scanning dependencies of target onlinehelp-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/onlinehelp/tests/helpformat.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/functions.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/functions.cpp /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/options/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/options/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color= cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdspan/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/extensions.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdspan/tests/extensions.cpp Scanning dependencies of target options-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/options/tests/abstractoptionstorage.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/onlinehelp/tests/helpmanager.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdspan/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/layouts.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdspan/tests/layouts.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/gausstransform.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/gausstransform.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/onlinehelp/tests/helpwritercontext.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdspan/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/mdspan.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdspan/tests/mdspan.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.a ../../../../lib/libgtest.a -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 86%] Built target onlinehelp-test /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/pbcutil/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/pbcutil/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake --color= Scanning dependencies of target pbcutil-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/pbcutil/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/pbcutil/tests/pbc.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/options/tests/filenameoption.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/pbcutil/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/pbcutil/tests/pbcenums.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/densityfittingforce.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/pbcutil/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pbcutil-test.dir/pbc.cpp.o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 86%] Built target pbcutil-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/invertmatrix.cpp /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/random/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/random/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color= Scanning dependencies of target random-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/random/tests/exponentialdistribution.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/options/tests/filenameoptionmanager.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/matrix.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/matrix.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/random/tests/gammadistribution.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdspan/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o CMakeFiles/mdspan-test.dir/extents.cpp.o CMakeFiles/mdspan-test.dir/extensions.cpp.o CMakeFiles/mdspan-test.dir/layouts.cpp.o CMakeFiles/mdspan-test.dir/mdspan.cpp.o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/option.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/options/tests/option.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/multidimarray.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/random/tests/normaldistribution.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 86%] Built target mdspan-test /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/restraint/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/restraint/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color= Scanning dependencies of target restraintpotential-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/restraint/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/restraint/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/restraint/tests/manager.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/options/tests/optionsassigner.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/restraint/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/restraint/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/restraintpotential-test.dir/manager.cpp.o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/seed.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/random/tests/seed.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 86%] Built target restraintpotential-test /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/tables/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/tables/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color= Scanning dependencies of target table-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/tables/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/tables/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/tables/tests/splinetable.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/random/tests/tabulatednormaldistribution.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/paddedvector.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/threefry.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/random/tests/threefry.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/options/tests/repeatingsection.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/random/tests/uniformintdistribution.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/tables/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/tables/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/options/tests/timeunitmanager.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/table-test.dir/splinetable.cpp.o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 86%] Built target table-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/random/tests/uniformrealdistribution.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/taskassignment/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/taskassignment/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color= Scanning dependencies of target taskassignment-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/taskassignment/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/taskassignment/tests/usergpuids.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/options/tests/treesupport.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/random-test.dir/exponentialdistribution.cpp.o CMakeFiles/random-test.dir/gammadistribution.cpp.o CMakeFiles/random-test.dir/normaldistribution.cpp.o CMakeFiles/random-test.dir/seed.cpp.o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o CMakeFiles/random-test.dir/threefry.cpp.o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 87%] Built target random-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/vectypes.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/topology/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/topology/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake --color= Scanning dependencies of target topology-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/topology/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/topology/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/topology/tests/exclusionblocks.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/taskassignment/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/topology/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/topology/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/topology/tests/mtop.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o CMakeFiles/options-test.dir/filenameoption.cpp.o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o CMakeFiles/options-test.dir/option.cpp.o CMakeFiles/options-test.dir/optionsassigner.cpp.o CMakeFiles/options-test.dir/repeatingsection.cpp.o CMakeFiles/options-test.dir/timeunitmanager.cpp.o CMakeFiles/options-test.dir/treesupport.cpp.o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 88%] Built target taskassignment-test /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/pulling/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/pulling/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color= Scanning dependencies of target pull-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/pulling/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/pulling/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pull-test.dir/pull.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/pulling/tests/pull.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o CMakeFiles/math-test.dir/densityfit.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/gausstransform.cpp.o CMakeFiles/math-test.dir/densityfittingforce.cpp.o CMakeFiles/math-test.dir/invertmatrix.cpp.o CMakeFiles/math-test.dir/matrix.cpp.o CMakeFiles/math-test.dir/multidimarray.cpp.o CMakeFiles/math-test.dir/paddedvector.cpp.o CMakeFiles/math-test.dir/vectypes.cpp.o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 89%] Built target options-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/pulling/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/pulling/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 91%] Built target math-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/topology/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/topology/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/topology/tests/symtab.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/topology/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/topology/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/awh/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/awh/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color= Scanning dependencies of target awh-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/awh/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/bias.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/awh/tests/bias.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pull-test.dir/pull.cpp.o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/simd/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color= Scanning dependencies of target simd-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/bootstrap_loadstore.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 92%] Built target pull-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/awh/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/awh/tests/biasstate.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/base.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/base.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/topology-test.dir/exclusionblocks.cpp.o CMakeFiles/topology-test.dir/mtop.cpp.o CMakeFiles/topology-test.dir/symtab.cpp.o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 93%] Built target topology-test /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/compat/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/compat/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color= Scanning dependencies of target compat-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/compat/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-unused-member-function -o CMakeFiles/compat-test.dir/optional.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/compat/tests/optional.cpp /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color= Scanning dependencies of target fileio-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio/tests/confio.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/awh/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/grid.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/awh/tests/grid.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/awh/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio/tests/filemd5.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd_floatingpoint.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/grid.cpp.o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/awh-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio/tests/mrcserializer.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 94%] Built target awh-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd_floatingpoint_util.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio/tests/mrcdensitymap.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd_vector_operations.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd_math.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/compat/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/compat/tests/pointers.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio/tests/mrcdensitymapheader.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd_memory.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/compat/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/string_view.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/compat/tests/string_view.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio/tests/readinp.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio/tests/fileioxdrserializer.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio/tests/tngio.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd_integer.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd4.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd4_floatingpoint.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 95%] Built target fileio-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd4_vector_operations.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/compat/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd4_math.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/scalar.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/compat-test.dir/optional.cpp.o CMakeFiles/compat-test.dir/pointers.cpp.o CMakeFiles/compat-test.dir/string_view.cpp.o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 96%] Built target compat-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/scalar_util.cpp /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color= Scanning dependencies of target commandline-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/scalar_math.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdrunutility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-mpi-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/base.cpp.o CMakeFiles/simd-test.dir/simd.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4_math.cpp.o CMakeFiles/simd-test.dir/scalar.cpp.o CMakeFiles/simd-test.dir/scalar_util.cpp.o CMakeFiles/simd-test.dir/scalar_math.cpp.o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgtest.a -lpthread cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdrunutility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color= [ 98%] Built target simd-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp Scanning dependencies of target mdrunutility-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdrunutility/tests/threadaffinity.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.a ../../../../lib/libgtest.a -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 98%] Built target mdrunutility-mpi-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/tests/cmdlineparser.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.a ../../../../lib/libgtest.a -lpthread cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/filenm.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/tests/filenm.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 98%] Built target mdrunutility-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/tests/pargs.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o CMakeFiles/commandline-test.dir/filenm.cpp.o CMakeFiles/commandline-test.dir/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.so ../../../../lib/libgmock.a ../../../../lib/libgtest.a -lpthread make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [100%] Built target commandline-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/CMakeFiles/tests.dir/DependInfo.cmake --color= Scanning dependencies of target tests make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [100%] Built target tests make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/cmake -E cmake_progress_start /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/CMakeFiles 0 make[2]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' make[1]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' (cd build/mpich; LD_LIBRARY_PATH=/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/lib \ ctest -V || dpkg-architecture -i hurd-i386 || dpkg-architecture -i s390x ) UpdateCTestConfiguration from :/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/DartConfiguration.tcl Parse Config file:/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/DartConfiguration.tcl UpdateCTestConfiguration from :/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/DartConfiguration.tcl Parse Config file:/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/DartConfiguration.tcl Test project /build/gromacs-5atmZb/gromacs-2020.6/build/mpich Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: TestUtilsUnitTests 1: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/bin/testutils-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/Testing/Temporary/TestUtilsUnitTests.xml" 1: Test timeout computed to be: 30 1: [==========] Running 59 tests from 5 test cases. 1: [----------] Global test environment set-up. 1: [----------] 10 tests from InteractiveTestHelperTest 1: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 1: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (1 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (0 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 1: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 1: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 1: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) 1: [----------] 10 tests from InteractiveTestHelperTest (5 ms total) 1: 1: [----------] 34 tests from ReferenceDataTest 1: [ RUN ] ReferenceDataTest.HandlesSimpleData 1: [ OK ] ReferenceDataTest.HandlesSimpleData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 1: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 1: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesStringBlockData 1: [ OK ] ReferenceDataTest.HandlesStringBlockData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesVectorData 1: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceData 1: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 1: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesIncorrectData 1: [ OK ] ReferenceDataTest.HandlesIncorrectData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 1: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesMissingData 1: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedData 1: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesAnys 1: [ OK ] ReferenceDataTest.HandlesAnys (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 1: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue 1: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType 1: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 1: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 1: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 1: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 1: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 1: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 1: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 1: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 1: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 1: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesReadingValues 1: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (0 ms) 1: [----------] 34 tests from ReferenceDataTest (12 ms total) 1: 1: [----------] 7 tests from FloatingPointDifferenceTest 1: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 1: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 1: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 1: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 1: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 1: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 1: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 1: 1: [----------] 4 tests from FloatingPointToleranceTest 1: [ RUN ] FloatingPointToleranceTest.UlpTolerance 1: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 1: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 1: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 1: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 1: 1: [----------] 4 tests from XvgTests 1: [ RUN ] XvgTests.CreateFile 1: [ OK ] XvgTests.CreateFile (1 ms) 1: [ RUN ] XvgTests.CheckMissing 1: [ OK ] XvgTests.CheckMissing (1 ms) 1: [ RUN ] XvgTests.CheckExtra 1: [ OK ] XvgTests.CheckExtra (0 ms) 1: [ RUN ] XvgTests.ReadIncorrect 1: [ OK ] XvgTests.ReadIncorrect (0 ms) 1: [----------] 4 tests from XvgTests (2 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 59 tests from 5 test cases ran. (19 ms total) 1: [ PASSED ] 59 tests. 1/30 Test #1: TestUtilsUnitTests ............... Passed 0.10 sec test 2 Start 2: TestUtilsMpiUnitTests 2: Test command: /usr/bin/mpiexec.mpich "-np" "2" "-host" "localhost" "/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/bin/testutils-mpi-test" "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/Testing/Temporary/TestUtilsMpiUnitTests.xml" 2: Test timeout computed to be: 30 2: [==========] Running 1 test from 1 test case. 2: [----------] Global test environment set-up. 2: [----------] 1 test from MpiSelfTest 2: [ RUN ] MpiSelfTest.Runs 2: [ OK ] MpiSelfTest.Runs (1 ms) 2: [----------] 1 test from MpiSelfTest (1 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 1 test from 1 test case ran. (1 ms total) 2: [ PASSED ] 1 test. 2/30 Test #2: TestUtilsMpiUnitTests ............ Passed 0.11 sec test 3 Start 3: UtilityUnitTests 3: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/bin/utility-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/Testing/Temporary/UtilityUnitTests.xml" 3: Test timeout computed to be: 30 3: [==========] Running 347 tests from 56 test cases. 3: [----------] Global test environment set-up. 3: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 3: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/0.Move 3: [ OK ] AllocatorTest/0.Move (0 ms) 3: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/0 (0 ms total) 3: 3: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 3: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/1.Move 3: [ OK ] AllocatorTest/1.Move (0 ms) 3: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/1 (0 ms total) 3: 3: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 3: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/2.Move 3: [ OK ] AllocatorTest/2.Move (0 ms) 3: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/2 (0 ms total) 3: 3: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 3: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/3.Move 3: [ OK ] AllocatorTest/3.Move (0 ms) 3: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/3 (0 ms total) 3: 3: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 3: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (1 ms) 3: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/4.Move 3: [ OK ] AllocatorTest/4.Move (0 ms) 3: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/4 (1 ms total) 3: 3: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 3: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/5.Move 3: [ OK ] AllocatorTest/5.Move (0 ms) 3: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/5 (0 ms total) 3: 3: [----------] 1 test from AllocatorUntypedTest 3: [ RUN ] AllocatorUntypedTest.Comparison 3: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 3: [----------] 1 test from AllocatorUntypedTest (0 ms total) 3: 3: [----------] 1 test from EmptyArrayRefTest 3: [ RUN ] EmptyArrayRefTest.IsEmpty 3: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 3: [----------] 1 test from EmptyArrayRefTest (0 ms total) 3: 3: [----------] 1 test from EmptyConstArrayRefTest 3: [ RUN ] EmptyConstArrayRefTest.IsEmpty 3: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 3: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (1 ms) 3: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/8 (1 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/14 (1 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 3: 3: [----------] 2 tests from CStringUtilityTest 3: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison 3: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) 3: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength 3: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms) 3: [----------] 2 tests from CStringUtilityTest (0 ms total) 3: 3: [----------] 2 tests from DefaultInitializationAllocator 3: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization 3: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) 3: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization 3: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) 3: [----------] 2 tests from DefaultInitializationAllocator (0 ms total) 3: 3: [----------] 4 tests from EnumerationHelpersTest 3: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks 3: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms) 3: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks 3: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) 3: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe 3: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) 3: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks 3: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) 3: [----------] 4 tests from EnumerationHelpersTest (0 ms total) 3: 3: [----------] 9 tests from FixedCapacityVectorTest 3: [ RUN ] FixedCapacityVectorTest.IsEmpty 3: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) 3: [ RUN ] FixedCapacityVectorTest.PushWorks 3: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.PopWorks 3: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.ClearWorks 3: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks 3: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.AtThrows 3: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms) 3: [ RUN ] FixedCapacityVectorTest.IteratorWorks 3: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks 3: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks 3: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) 3: [----------] 9 tests from FixedCapacityVectorTest (1 ms total) 3: 3: [----------] 5 tests from InMemorySerializerTest 3: [ RUN ] InMemorySerializerTest.Roundtrip 3: [ OK ] InMemorySerializerTest.Roundtrip (0 ms) 3: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap 3: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) 3: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap 3: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) 3: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap 3: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms) 3: [ RUN ] InMemorySerializerTest.SizeIsCorrect 3: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) 3: [----------] 5 tests from InMemorySerializerTest (0 ms total) 3: 3: [----------] 4 tests from KeyValueTreeSerializerTest 3: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 3: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms) 3: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 3: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) 3: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 3: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms) 3: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 3: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) 3: [----------] 4 tests from KeyValueTreeSerializerTest (0 ms total) 3: 3: [----------] 6 tests from TreeValueTransformTest 3: [ RUN ] TreeValueTransformTest.SimpleTransforms 3: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) 3: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 3: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (1 ms) 3: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 3: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms) 3: [ RUN ] TreeValueTransformTest.ObjectFromString 3: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) 3: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 3: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) 3: [ RUN ] TreeValueTransformTest.ScopedTransformRules 3: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 3: [----------] 6 tests from TreeValueTransformTest (1 ms total) 3: 3: [----------] 1 test from TreeValueTransformErrorTest 3: [ RUN ] TreeValueTransformErrorTest.ConversionError 3: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms) 3: [----------] 1 test from TreeValueTransformErrorTest (0 ms total) 3: 3: [----------] 7 tests from LoggerTest 3: [ RUN ] LoggerTest.EmptyLoggerWorks 3: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 3: [ RUN ] LoggerTest.LogsToStream 3: [ OK ] LoggerTest.LogsToStream (0 ms) 3: [ RUN ] LoggerTest.LogsToFile 3: [ OK ] LoggerTest.LogsToFile (6 ms) 3: [ RUN ] LoggerTest.LevelFilteringWorks 3: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 3: [ RUN ] LoggerTest.LogsToMultipleStreams 3: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 3: [ RUN ] LoggerTest.LogsToMultipleFiles 3: [ OK ] LoggerTest.LogsToMultipleFiles (1 ms) 3: [ RUN ] LoggerTest.LogsToStreamAndFile 3: [ OK ] LoggerTest.LogsToStreamAndFile (0 ms) 3: [----------] 7 tests from LoggerTest (7 ms total) 3: 3: [----------] 4 tests from MutexBasicTest 3: [ RUN ] MutexBasicTest.CanBeMade 3: [ OK ] MutexBasicTest.CanBeMade (0 ms) 3: [ RUN ] MutexBasicTest.CanBeLocked 3: [ OK ] MutexBasicTest.CanBeLocked (0 ms) 3: [ RUN ] MutexBasicTest.CanBeTryLocked 3: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms) 3: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard 3: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms) 3: [----------] 4 tests from MutexBasicTest (0 ms total) 3: 3: [----------] 3 tests from MutexTaskTest 3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock 3: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (1 ms) 3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread 3: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (0 ms) 3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread 3: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms) 3: [----------] 3 tests from MutexTaskTest (1 ms total) 3: 3: [----------] 2 tests from PathTest 3: [ RUN ] PathTest.StripSourcePrefixWorks 3: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 3: [ RUN ] PathTest.SearchOperationsWork 3: [ OK ] PathTest.SearchOperationsWork (1 ms) 3: [----------] 2 tests from PathTest (1 ms total) 3: 3: [----------] 2 tests from PhysicalNodeCommunicatorTest 3: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 3: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 3: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 3: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 3: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 3: 3: [----------] 9 tests from StringUtilityTest 3: [ RUN ] StringUtilityTest.StartsWith 3: [ OK ] StringUtilityTest.StartsWith (0 ms) 3: [ RUN ] StringUtilityTest.EndsWith 3: [ OK ] StringUtilityTest.EndsWith (0 ms) 3: [ RUN ] StringUtilityTest.StripSuffixIfPresent 3: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 3: [ RUN ] StringUtilityTest.StripString 3: [ OK ] StringUtilityTest.StripString (0 ms) 3: [ RUN ] StringUtilityTest.SplitString 3: [ OK ] StringUtilityTest.SplitString (0 ms) 3: [ RUN ] StringUtilityTest.SplitDelimitedString 3: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 3: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 3: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) 3: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive 3: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) 3: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength 3: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) 3: [----------] 9 tests from StringUtilityTest (1 ms total) 3: 3: [----------] 2 tests from FormatStringTest 3: [ RUN ] FormatStringTest.HandlesBasicFormatting 3: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 3: [ RUN ] FormatStringTest.HandlesLongStrings 3: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 3: [----------] 2 tests from FormatStringTest (0 ms total) 3: 3: [----------] 1 test from StringFormatterTest 3: [ RUN ] StringFormatterTest.HandlesBasicFormatting 3: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 3: [----------] 1 test from StringFormatterTest (0 ms total) 3: 3: [----------] 1 test from formatAndJoinTest 3: [ RUN ] formatAndJoinTest.Works 3: [ OK ] formatAndJoinTest.Works (0 ms) 3: [----------] 1 test from formatAndJoinTest (0 ms total) 3: 3: [----------] 1 test from JoinStringsTest 3: [ RUN ] JoinStringsTest.Works 3: [ OK ] JoinStringsTest.Works (0 ms) 3: [----------] 1 test from JoinStringsTest (0 ms total) 3: 3: [----------] 6 tests from ReplaceAllTest 3: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 3: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesNoMatches 3: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 3: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 3: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 3: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 3: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 3: [----------] 6 tests from ReplaceAllTest (0 ms total) 3: 3: [----------] 10 tests from TextLineWrapperTest 3: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 3: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 3: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 3: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 3: [ RUN ] TextLineWrapperTest.WrapsCorrectly 3: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms) 3: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 3: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesIndent 3: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 3: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 3: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 3: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) 3: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 3: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) 3: [----------] 10 tests from TextLineWrapperTest (0 ms total) 3: 3: [----------] 6 tests from TextWriterTest 3: [ RUN ] TextWriterTest.WritesLines 3: [ OK ] TextWriterTest.WritesLines (0 ms) 3: [ RUN ] TextWriterTest.WritesLinesInParts 3: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 3: [ RUN ] TextWriterTest.WritesWrappedLines 3: [ OK ] TextWriterTest.WritesWrappedLines (1 ms) 3: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 3: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 3: [ RUN ] TextWriterTest.TracksNewlines 3: [ OK ] TextWriterTest.TracksNewlines (0 ms) 3: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 3: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 3: [----------] 6 tests from TextWriterTest (1 ms total) 3: 3: [----------] 1 test from TypeTraitsTest 3: [ RUN ] TypeTraitsTest.IsIntegralConstant 3: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 3: [----------] 1 test from TypeTraitsTest (0 ms total) 3: 3: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 3: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 3: 3: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 3: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 3: 3: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 3: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 3: 3: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms) 3: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (1 ms total) 3: 3: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 3: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (0 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 347 tests from 56 test cases ran. (20 ms total) 3: [ PASSED ] 347 tests. 3/30 Test #3: UtilityUnitTests ................. Passed 0.06 sec test 4 Start 4: UtilityMpiUnitTests 4: Test command: /usr/bin/mpiexec.mpich "-np" "4" "-host" "localhost" "/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/bin/utility-mpi-test" "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/Testing/Temporary/UtilityMpiUnitTests.xml" 4: Test timeout computed to be: 30 4: [==========] Running 2 tests from 1 test case. 4: [----------] Global test environment set-up. 4: [----------] 2 tests from PhysicalNodeCommunicatorTest 4: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 4: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 4: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 4: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 4: [----------] 2 tests from PhysicalNodeCommunicatorTest (1 ms total) 4: 4: [----------] Global test environment tear-down 4: [==========] 2 tests from 1 test case ran. (2 ms total) 4: [ PASSED ] 2 tests. 4/30 Test #4: UtilityMpiUnitTests .............. Passed 0.17 sec test 5 Start 5: MdlibUnitTest 5: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/bin/mdlib-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/Testing/Temporary/MdlibUnitTest.xml" 5: Test timeout computed to be: 30 5: [==========] Running 187 tests from 13 test cases. 5: [----------] Global test environment set-up. 5: [----------] 1 test from VerletBufferConstraintTest 5: [ RUN ] VerletBufferConstraintTest.EqualMasses 5: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 5: [----------] 1 test from VerletBufferConstraintTest (0 ms total) 5: 5: [----------] 2 tests from PrEbinTest 5: [ RUN ] PrEbinTest.HandlesAverages 5: [ OK ] PrEbinTest.HandlesAverages (0 ms) 5: [ RUN ] PrEbinTest.HandlesEmptyAverages 5: [ OK ] PrEbinTest.HandlesEmptyAverages (0 ms) 5: [----------] 2 tests from PrEbinTest (0 ms total) 5: 5: [----------] 4 tests from ShakeTest 5: [ RUN ] ShakeTest.ConstrainsOneBond 5: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) 5: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 5: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 5: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 5: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 5: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 5: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 5: [----------] 4 tests from ShakeTest (0 ms total) 5: 5: [----------] 1 test from NullSignalTest 5: [ RUN ] NullSignalTest.NullSignallerWorks 5: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 5: [----------] 1 test from NullSignalTest (0 ms total) 5: 5: [----------] 7 tests from SignalTest 5: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 5: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 5: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 5: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 5: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 5: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 5: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 5: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 5: [----------] 7 tests from SignalTest (0 ms total) 5: 5: [----------] 9 tests from UpdateGroups 5: [ RUN ] UpdateGroups.ethaneUA 5: [ OK ] UpdateGroups.ethaneUA (0 ms) 5: [ RUN ] UpdateGroups.methane 5: [ OK ] UpdateGroups.methane (0 ms) 5: [ RUN ] UpdateGroups.ethane 5: [ OK ] UpdateGroups.ethane (0 ms) 5: [ RUN ] UpdateGroups.butaneUA 5: [ OK ] UpdateGroups.butaneUA (0 ms) 5: [ RUN ] UpdateGroups.waterThreeSite 5: [ OK ] UpdateGroups.waterThreeSite (0 ms) 5: [ RUN ] UpdateGroups.waterFourSite 5: [ OK ] UpdateGroups.waterFourSite (0 ms) 5: [ RUN ] UpdateGroups.fourAtomsWithSettle 5: [ OK ] UpdateGroups.fourAtomsWithSettle (0 ms) 5: [ RUN ] UpdateGroups.waterFlexAngle 5: [ OK ] UpdateGroups.waterFlexAngle (0 ms) 5: [ RUN ] UpdateGroups.twoMoltypes 5: [ OK ] UpdateGroups.twoMoltypes (0 ms) 5: [----------] 9 tests from UpdateGroups (0 ms total) 5: 5: [----------] 1 test from UpdateGroupsCog 5: [ RUN ] UpdateGroupsCog.ComputesCogs 5: [ OK ] UpdateGroupsCog.ComputesCogs (1 ms) 5: [----------] 1 test from UpdateGroupsCog (1 ms total) 5: 5: [----------] 84 tests from WithParameters/ConstraintsTest 5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/0 5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/1 5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/2 5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/3 5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/2 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/3 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/4 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/5 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/6 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/7 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1 (1 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/2 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/3 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/4 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/5 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/6 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/7 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/8 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/8 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/9 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/9 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/10 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/10 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/11 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/11 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/2 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/3 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/4 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/5 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/6 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/7 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/8 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/8 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/9 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/9 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/10 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/10 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/11 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/11 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/12 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/12 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/13 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/13 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/14 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/14 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/15 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/15 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/0 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/1 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/2 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/3 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/4 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/5 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/6 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/7 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/8 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/8 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/9 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/9 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/10 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/10 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/11 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/11 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/12 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/12 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/13 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/13 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/14 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/14 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/15 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/15 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/16 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/16 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/17 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/17 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/18 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/18 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/19 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/19 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/0 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/0 (1 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/1 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/2 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/3 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/4 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/5 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/6 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/7 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/8 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/8 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/9 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/9 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/10 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/10 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/11 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/11 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/12 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/12 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/13 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/13 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/14 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/14 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/15 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/15 (1 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/16 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/16 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/17 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/17 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/18 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/18 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/19 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/19 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/20 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/20 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/21 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/21 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/22 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/22 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/23 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/23 (0 ms) 5: [----------] 84 tests from WithParameters/ConstraintsTest (4 ms total) 5: 5: [----------] 11 tests from WithParameters/EnergyOutputTest 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (2 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (1 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (1 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3 5: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (1 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as single precision energy file 5: Reading energy frame 0 time 10.100 Reading energy frame 1 time 27.500 Reading energy frame 2 time 44.900 Reading energy frame 3 time 62.300 Reading energy frame 4 time 79.700 Reading energy frame 5 time 97.100 Reading energy frame 6 time 114.500 Reading energy frame 7 time 131.900 Reading energy frame 8 time 149.300 Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (6 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (5 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (4 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (4 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (4 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (6 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (3 ms) 5: [----------] 11 tests from WithParameters/EnergyOutputTest (92 ms total) 5: 5: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms) 5: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (1 ms total) 5: 5: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms) 5: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (0 ms total) 5: 5: [----------] 16 tests from WithParameters/LeapFrogTest 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (1 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (1 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (1 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (3 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (7 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (1 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (2 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (2 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (1 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (2 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (2 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (2 ms) 5: [----------] 16 tests from WithParameters/LeapFrogTest (28 ms total) 5: 5: [----------] 13 tests from WithParameters/SettleTest 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (1 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (1 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (1 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (1 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (2 ms) 5: [----------] 13 tests from WithParameters/SettleTest (9 ms total) 5: 5: [----------] Global test environment tear-down 5: [==========] 187 tests from 13 test cases ran. (136 ms total) 5: [ PASSED ] 187 tests. 5/30 Test #5: MdlibUnitTest .................... Passed 0.17 sec test 6 Start 6: AppliedForcesUnitTest 6: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/bin/applied_forces-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/Testing/Temporary/AppliedForcesUnitTest.xml" 6: Test timeout computed to be: 30 6: [==========] Running 20 tests from 4 test cases. 6: [----------] Global test environment set-up. 6: [----------] 2 tests from DensityFittingTest 6: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows 6: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (0 ms) 6: [ RUN ] DensityFittingTest.SingleAtom 6: [ OK ] DensityFittingTest.SingleAtom (1 ms) 6: [----------] 2 tests from DensityFittingTest (1 ms total) 6: 6: [----------] 8 tests from DensityFittingOptionsTest 6: [ RUN ] DensityFittingOptionsTest.DefaultParameters 6: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) 6: [ RUN ] DensityFittingOptionsTest.OptionSetsActive 6: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms) 6: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive 6: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 6: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive 6: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (0 ms) 6: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup 6: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 6: [ RUN ] DensityFittingOptionsTest.InternalsToKvt 6: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) 6: [ RUN ] DensityFittingOptionsTest.KvtToInternal 6: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms) 6: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent 6: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms) 6: [----------] 8 tests from DensityFittingOptionsTest (1 ms total) 6: 6: [----------] 7 tests from DensityFittingAmplitudeLookupTest 6: [ RUN ] DensityFittingAmplitudeLookupTest.Unity 6: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.Charge 6: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.Masses 6: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign 6: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct 6: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign 6: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct 6: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) 6: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total) 6: 6: [----------] 3 tests from ElectricFieldTest 6: [ RUN ] ElectricFieldTest.Static 6: [ OK ] ElectricFieldTest.Static (0 ms) 6: [ RUN ] ElectricFieldTest.Oscillating 6: [ OK ] ElectricFieldTest.Oscillating (0 ms) 6: [ RUN ] ElectricFieldTest.Pulsed 6: [ OK ] ElectricFieldTest.Pulsed (0 ms) 6: [----------] 3 tests from ElectricFieldTest (0 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 20 tests from 4 test cases ran. (2 ms total) 6: [ PASSED ] 20 tests. 6/30 Test #6: AppliedForcesUnitTest ............ Passed 0.04 sec test 7 Start 7: CommandLineUnitTests 7: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/bin/commandline-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/Testing/Temporary/CommandLineUnitTests.xml" 7: Test timeout computed to be: 30 7: [==========] Running 59 tests from 7 test cases. 7: [----------] Global test environment set-up. 7: [----------] 3 tests from CommandLineHelpModuleTest 7: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 7: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (0 ms) 7: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 7: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (1 ms) 7: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 7: [ OK ] CommandLineHelpModuleTest.ExportsHelp (1 ms) 7: [----------] 3 tests from CommandLineHelpModuleTest (2 ms total) 7: 7: [----------] 7 tests from CommandLineHelpWriterTest 7: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 7: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (0 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 7: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 7: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 7: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 7: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 7: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (1 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues 7: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms) 7: [----------] 7 tests from CommandLineHelpWriterTest (1 ms total) 7: 7: [----------] 6 tests from CommandLineModuleManagerTest 7: [ RUN ] CommandLineModuleManagerTest.RunsModule 7: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) 7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 7: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 7: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 7: [----------] 6 tests from CommandLineModuleManagerTest (0 ms total) 7: 7: [----------] 13 tests from CommandLineParserTest 7: [ RUN ] CommandLineParserTest.HandlesSingleValues 7: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 7: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 7: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (1 ms) 7: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 7: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 7: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesString 7: [ OK ] CommandLineParserTest.HandlesString (0 ms) 7: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 7: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 7: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 7: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 7: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 7: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 7: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 7: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 7: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 7: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 7: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 7: [----------] 13 tests from CommandLineParserTest (1 ms total) 7: 7: [----------] 6 tests from CommandLineProgramContextTest 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 7: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 7: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 7: [----------] 6 tests from CommandLineProgramContextTest (0 ms total) 7: 7: [----------] 3 tests from OutputNamesTest 7: [ RUN ] OutputNamesTest.CanBeSuffixed 7: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) 7: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend 7: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) 7: [ RUN ] OutputNamesTest.CanHavePartNumberAdded 7: [ OK ] OutputNamesTest.CanHavePartNumberAdded (1 ms) 7: [----------] 3 tests from OutputNamesTest (1 ms total) 7: 7: [----------] 21 tests from ParseCommonArgsTest 7: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 7: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 7: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 7: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 7: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 7: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 7: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 7: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 7: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 7: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 7: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 7: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 7: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 7: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 7: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 7: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 7: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 7: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (1 ms) 7: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 7: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 7: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 7: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (0 ms) 7: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 7: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (1 ms) 7: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 7: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (1 ms) 7: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 7: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (1 ms) 7: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 7: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 7: [----------] 21 tests from ParseCommonArgsTest (4 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 59 tests from 7 test cases ran. (9 ms total) 7: [ PASSED ] 59 tests. 7/30 Test #7: CommandLineUnitTests ............. Passed 0.03 sec test 8 Start 8: DomDecTests 8: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/bin/domdec-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/Testing/Temporary/DomDecTests.xml" 8: Test timeout computed to be: 30 8: [==========] Running 9 tests from 2 test cases. 8: [----------] Global test environment set-up. 8: [----------] 7 tests from HashedMap 8: [ RUN ] HashedMap.InsertsFinds 8: [ OK ] HashedMap.InsertsFinds (0 ms) 8: [ RUN ] HashedMap.NegativeKeysWork 8: [ OK ] HashedMap.NegativeKeysWork (0 ms) 8: [ RUN ] HashedMap.InsertsErases 8: [ OK ] HashedMap.InsertsErases (0 ms) 8: [ RUN ] HashedMap.InsertsOrAssigns 8: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 8: [ RUN ] HashedMap.Clears 8: [ OK ] HashedMap.Clears (0 ms) 8: [ RUN ] HashedMap.LinkedEntries 8: [ OK ] HashedMap.LinkedEntries (0 ms) 8: [ RUN ] HashedMap.ResizesTable 8: [ OK ] HashedMap.ResizesTable (0 ms) 8: [----------] 7 tests from HashedMap (0 ms total) 8: 8: [----------] 2 tests from LocalAtomSetManager 8: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 8: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 8: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 8: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 8: [----------] 2 tests from LocalAtomSetManager (0 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 9 tests from 2 test cases ran. (0 ms total) 8: [ PASSED ] 9 tests. 8/30 Test #8: DomDecTests ...................... Passed 0.02 sec test 9 Start 9: EwaldUnitTests 9: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/bin/ewald-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/Testing/Temporary/EwaldUnitTests.xml" 9: Test timeout computed to be: 30 9: [==========] Running 257 tests from 10 test cases. 9: [----------] Global test environment set-up. 9: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (4 ms) 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 9: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (4 ms total) 9: 9: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (5 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (3 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (1 ms) 9: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (34 ms total) 9: 9: [----------] 144 tests from SaneInput/PmeGatherTest 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/72 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/72 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/73 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/73 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/74 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/74 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/75 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/75 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/76 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/76 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/77 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/77 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/78 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/78 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/79 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/79 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/80 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/80 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/81 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/81 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/82 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/82 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/83 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/83 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/84 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/84 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/85 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/85 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/86 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/86 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/87 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/87 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/88 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/88 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/89 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/89 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/90 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/90 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/91 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/91 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/92 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/92 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/93 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/93 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/94 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/94 (5 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/95 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/95 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/96 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/96 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/97 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/97 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/98 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/98 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/99 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/99 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/100 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/100 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/101 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/101 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/102 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/102 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/103 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/103 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/104 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/104 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/105 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/105 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/106 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/106 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/107 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/107 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/108 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/108 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/109 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/109 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/110 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/110 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/111 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/111 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/112 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/112 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/113 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/113 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/114 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/114 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/115 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/115 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/116 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/116 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/117 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/117 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/118 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/118 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/119 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/119 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/120 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/120 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/121 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/121 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/122 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/122 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/123 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/123 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/124 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/124 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/125 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/125 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/126 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/126 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/127 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/127 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/128 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/128 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/129 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/129 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/130 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/130 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/131 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/131 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/132 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/132 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/133 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/133 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/134 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/134 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/135 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/135 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/136 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/136 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/137 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/137 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/138 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/138 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/139 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/139 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/140 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/140 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/141 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/141 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/142 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/142 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/143 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/143 (1 ms) 9: [----------] 144 tests from SaneInput/PmeGatherTest (59 ms total) 9: 9: [----------] 16 tests from SaneInput/PmeSolveTest 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (2 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (2 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (2 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (0 ms) 9: [----------] 16 tests from SaneInput/PmeSolveTest (19 ms total) 9: 9: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (0 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (0 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (0 ms) 9: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (5 ms total) 9: 9: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (2 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (1 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (2 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (1 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (1 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (2 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (0 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (0 ms) 9: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (11 ms total) 9: 9: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (0 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (2 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (0 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (2 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (0 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (0 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (2 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (0 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (0 ms) 9: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (13 ms total) 9: 9: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (1 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (33 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (1 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (2 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (2 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (2 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (2 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (1 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (2 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (1 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (2 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (2 ms) 9: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (51 ms total) 9: 9: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (2 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (2 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (2 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (2 ms) 9: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (18 ms total) 9: 9: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (2 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (2 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (5 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (5 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (5 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (5 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (1 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (2 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (3 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (37 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (7 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (7 ms) 9: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (85 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 257 tests from 10 test cases ran. (598 ms total) 9: [ PASSED ] 257 tests. 9/30 Test #9: EwaldUnitTests ................... Passed 0.67 sec test 10 Start 10: FFTUnitTests 10: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/bin/fft-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/Testing/Temporary/FFTUnitTests.xml" 10: Test timeout computed to be: 30 10: [==========] Running 14 tests from 4 test cases. 10: [----------] Global test environment set-up. 10: [----------] 2 tests from ManyFFTTest 10: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 10: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (6 ms) 10: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 10: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (46 ms) 10: [----------] 2 tests from ManyFFTTest (54 ms total) 10: 10: [----------] 1 test from FFTTest 10: [ RUN ] FFTTest.Real2DLength18_15Test 10: [ OK ] FFTTest.Real2DLength18_15Test (9 ms) 10: [----------] 1 test from FFTTest (9 ms total) 10: 10: [----------] 1 test from FFFTest3D 10: [ RUN ] FFFTest3D.Real5_6_9 10: [ OK ] FFFTest3D.Real5_6_9 (2 ms) 10: [----------] 1 test from FFFTest3D (3 ms total) 10: 10: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (1 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (1 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (3 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (8 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (2 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (1 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (1 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (1 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (19 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (48 ms) 10: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (86 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 14 tests from 4 test cases ran. (152 ms total) 10: [ PASSED ] 14 tests. 10/30 Test #10: FFTUnitTests ..................... Passed 0.17 sec test 11 Start 11: GpuUtilsUnitTests 11: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/bin/gpu_utils-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/Testing/Temporary/GpuUtilsUnitTests.xml" 11: Test timeout computed to be: 30 11: [==========] Running 62 tests from 20 test cases. 11: [----------] Global test environment set-up. 11: [----------] 2 tests from ClfftInitializer 11: [ RUN ] ClfftInitializer.SingleInitializationWorks 11: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) 11: [ RUN ] ClfftInitializer.TwoInitializationsWork 11: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) 11: [----------] 2 tests from ClfftInitializer (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 11: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 11: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 11: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 11: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float 11: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 11: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 11: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 11: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 11: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 11: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 11: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 11: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 11: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 11: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 11: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 11: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 11: 11: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 11: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 11: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (1 ms) 11: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 11: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 11: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 11: [----------] 3 tests from HostAllocatorTestCopyable/0 (1 ms total) 11: 11: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float 11: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 11: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 11: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 11: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 11: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 11: 11: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 11: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 11: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 11: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 11: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 11: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 11: 11: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 11: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 11: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 11: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 11: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/0.Swap 11: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/0.Comparison 11: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 11: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 11: 11: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float 11: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 11: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 11: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 11: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/1.Swap 11: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/1.Comparison 11: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 11: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 11: 11: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 11: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 11: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 11: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 11: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/2.Swap 11: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/2.Comparison 11: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 11: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 11: 11: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 11: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 11: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 11: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 11: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/3.Swap 11: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/3.Comparison 11: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 11: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 11: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 11: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 11: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float 11: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 11: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 11: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 11: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 11: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 11: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 11: 11: [----------] 1 test from HostAllocatorUntypedTest 11: [ RUN ] HostAllocatorUntypedTest.Comparison 11: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 11: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 11: 11: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 11: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/0.Move 11: [ OK ] AllocatorTest/0.Move (0 ms) 11: [----------] 4 tests from AllocatorTest/0 (0 ms total) 11: 11: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 11: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/1.Move 11: [ OK ] AllocatorTest/1.Move (0 ms) 11: [----------] 4 tests from AllocatorTest/1 (0 ms total) 11: 11: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 11: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/2.Move 11: [ OK ] AllocatorTest/2.Move (0 ms) 11: [----------] 4 tests from AllocatorTest/2 (0 ms total) 11: 11: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 11: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/3.Move 11: [ OK ] AllocatorTest/3.Move (0 ms) 11: [----------] 4 tests from AllocatorTest/3 (0 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 62 tests from 20 test cases ran. (1 ms total) 11: [ PASSED ] 62 tests. 11/30 Test #11: GpuUtilsUnitTests ................ Passed 0.02 sec test 12 Start 12: HardwareUnitTests 12: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/bin/hardware-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/Testing/Temporary/HardwareUnitTests.xml" 12: Test timeout computed to be: 30 12: [==========] Running 4 tests from 1 test case. 12: [----------] Global test environment set-up. 12: [----------] 4 tests from HardwareTopologyTest 12: [ RUN ] HardwareTopologyTest.Execute 12: [ OK ] HardwareTopologyTest.Execute (63 ms) 12: [ RUN ] HardwareTopologyTest.HwlocExecute 12: [ OK ] HardwareTopologyTest.HwlocExecute (49 ms) 12: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 12: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (50 ms) 12: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 12: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (46 ms) 12: [----------] 4 tests from HardwareTopologyTest (208 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 4 tests from 1 test case ran. (208 ms total) 12: [ PASSED ] 4 tests. 12/30 Test #12: HardwareUnitTests ................ Passed 0.23 sec test 13 Start 13: MathUnitTests 13: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/bin/math-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/Testing/Temporary/MathUnitTests.xml" 13: Test timeout computed to be: 30 13: [==========] Running 204 tests from 29 test cases. 13: [----------] Global test environment set-up. 13: [----------] 1 test from EmptyArrayRefWithPaddingTest 13: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 13: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 13: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 13: 13: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 13: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 13: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 13: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 13: 13: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 13: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 13: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 13: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 13: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 13: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 13: 13: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 13: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 13: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 13: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 13: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 13: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 13: 13: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 13: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 13: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 13: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 13: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 13: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 13: 13: [----------] 8 tests from TranslateAndScaleTest 13: [ RUN ] TranslateAndScaleTest.identityTransformation 13: [ OK ] TranslateAndScaleTest.identityTransformation (1 ms) 13: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling 13: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) 13: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation 13: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) 13: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial 13: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms) 13: [ RUN ] TranslateAndScaleTest.scalingIdentity 13: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms) 13: [ RUN ] TranslateAndScaleTest.scalingNonTrivial 13: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) 13: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero 13: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms) 13: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero 13: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) 13: [----------] 8 tests from TranslateAndScaleTest (1 ms total) 13: 13: [----------] 12 tests from DensitySimilarityTest 13: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect 13: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect 13: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch 13: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms) 13: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch 13: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (1 ms) 13: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect 13: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero 13: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms) 13: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect 13: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect 13: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne 13: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (43 ms) 13: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated 13: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (36 ms) 13: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated 13: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (47 ms) 13: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect 13: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms) 13: [----------] 12 tests from DensitySimilarityTest (128 ms total) 13: 13: [----------] 6 tests from StructureSimilarityTest 13: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 13: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 13: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 13: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 13: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 13: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 13: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 13: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 13: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 13: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 13: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 13: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 13: [----------] 6 tests from StructureSimilarityTest (0 ms total) 13: 13: [----------] 8 tests from ExponentialMovingAverage 13: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero 13: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) 13: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative 13: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) 13: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue 13: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) 13: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue 13: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) 13: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly 13: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) 13: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing 13: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) 13: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect 13: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) 13: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree 13: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) 13: [----------] 8 tests from ExponentialMovingAverage (0 ms total) 13: 13: [----------] 21 tests from FunctionTest 13: [ RUN ] FunctionTest.StaticLog2 13: [ OK ] FunctionTest.StaticLog2 (0 ms) 13: [ RUN ] FunctionTest.Log2I32Bit 13: [ OK ] FunctionTest.Log2I32Bit (0 ms) 13: [ RUN ] FunctionTest.Log2I64Bit 13: [ OK ] FunctionTest.Log2I64Bit (1 ms) 13: [ RUN ] FunctionTest.GreatestCommonDivisor 13: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 13: [ RUN ] FunctionTest.InvsqrtFloat 13: [ OK ] FunctionTest.InvsqrtFloat (0 ms) 13: [ RUN ] FunctionTest.InvsqrtDouble 13: [ OK ] FunctionTest.InvsqrtDouble (0 ms) 13: [ RUN ] FunctionTest.InvsqrtInteger 13: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 13: [ RUN ] FunctionTest.InvcbrtFloat 13: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 13: [ RUN ] FunctionTest.InvcbrtDouble 13: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 13: [ RUN ] FunctionTest.InvcbrtInteger 13: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 13: [ RUN ] FunctionTest.SixthrootFloat 13: [ OK ] FunctionTest.SixthrootFloat (1 ms) 13: [ RUN ] FunctionTest.SixthrootDouble 13: [ OK ] FunctionTest.SixthrootDouble (0 ms) 13: [ RUN ] FunctionTest.SixthrootInteger 13: [ OK ] FunctionTest.SixthrootInteger (0 ms) 13: [ RUN ] FunctionTest.InvsixthrootFloat 13: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 13: [ RUN ] FunctionTest.InvsixthrootDouble 13: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 13: [ RUN ] FunctionTest.InvsixthrootInteger 13: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 13: [ RUN ] FunctionTest.Powers 13: [ OK ] FunctionTest.Powers (0 ms) 13: [ RUN ] FunctionTest.ErfInvFloat 13: [ OK ] FunctionTest.ErfInvFloat (1 ms) 13: [ RUN ] FunctionTest.ErfInvDouble 13: [ OK ] FunctionTest.ErfInvDouble (0 ms) 13: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 13: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 13: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 13: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) 13: [----------] 21 tests from FunctionTest (3 ms total) 13: 13: [----------] 4 tests from GaussianOn1DLattice 13: [ RUN ] GaussianOn1DLattice.sumsCloseToOne 13: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) 13: [ RUN ] GaussianOn1DLattice.isCorrect 13: [ OK ] GaussianOn1DLattice.isCorrect (0 ms) 13: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero 13: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) 13: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange 13: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) 13: [----------] 4 tests from GaussianOn1DLattice (0 ms total) 13: 13: [----------] 9 tests from GaussTransformTest 13: [ RUN ] GaussTransformTest.isZeroUponConstruction 13: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) 13: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss 13: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) 13: [ RUN ] GaussTransformTest.isZeroAfterSettingZero 13: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) 13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX 13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) 13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY 13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) 13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ 13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) 13: [ RUN ] GaussTransformTest.complementaryGaussAddToZero 13: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) 13: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues 13: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms) 13: [ RUN ] GaussTransformTest.view 13: [ OK ] GaussTransformTest.view (0 ms) 13: [----------] 9 tests from GaussTransformTest (1 ms total) 13: 13: [----------] 3 tests from DensityFittingForce 13: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity 13: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) 13: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections 13: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) 13: [ RUN ] DensityFittingForce.pullsTowardsDerivative 13: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) 13: [----------] 3 tests from DensityFittingForce (0 ms total) 13: 13: [----------] 2 tests from InvertMatrixTest 13: [ RUN ] InvertMatrixTest.IdentityIsImpotent 13: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 13: [ RUN ] InvertMatrixTest.ComputesInverse 13: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 13: [----------] 2 tests from InvertMatrixTest (0 ms total) 13: 13: [----------] 2 tests from InvertBoxMatrixTest 13: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 13: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 13: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 13: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 13: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 13: 13: [----------] 15 tests from MatrixTest 13: [ RUN ] MatrixTest.canSetFromArray 13: [ OK ] MatrixTest.canSetFromArray (0 ms) 13: [ RUN ] MatrixTest.canSetStaticallyFromList 13: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) 13: [ RUN ] MatrixTest.canConstructAndFill 13: [ OK ] MatrixTest.canConstructAndFill (0 ms) 13: [ RUN ] MatrixTest.canSetValues 13: [ OK ] MatrixTest.canSetValues (0 ms) 13: [ RUN ] MatrixTest.canCopyAssign 13: [ OK ] MatrixTest.canCopyAssign (0 ms) 13: [ RUN ] MatrixTest.canSwap 13: [ OK ] MatrixTest.canSwap (0 ms) 13: [ RUN ] MatrixTest.staticMultiDimArrayExtent 13: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) 13: [ RUN ] MatrixTest.determinantWorks 13: [ OK ] MatrixTest.determinantWorks (0 ms) 13: [ RUN ] MatrixTest.noninvertableDeterminantIsZero 13: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) 13: [ RUN ] MatrixTest.determinantOfDiagonalMatrix 13: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) 13: [ RUN ] MatrixTest.traceWorks 13: [ OK ] MatrixTest.traceWorks (0 ms) 13: [ RUN ] MatrixTest.transposeWorks 13: [ OK ] MatrixTest.transposeWorks (0 ms) 13: [ RUN ] MatrixTest.transposeOfSymmetricMatrix 13: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) 13: [ RUN ] MatrixTest.canCreateFromLegacyMatrix 13: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) 13: [ RUN ] MatrixTest.canFillLegacyMatrix 13: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) 13: [----------] 15 tests from MatrixTest (0 ms total) 13: 13: [----------] 25 tests from MultiDimArrayTest 13: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic 13: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic 13: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canSetValuesInStatic 13: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic 13: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canMoveConstructStatic 13: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic 13: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canMoveAssignStatic 13: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic 13: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canCopyConstructStatic 13: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic 13: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canCopyAssignStatic 13: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic 13: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canSwapStatic 13: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canSwapDynamic 13: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent 13: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) 13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent 13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) 13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent 13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) 13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue 13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) 13: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray 13: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) 13: [ RUN ] MultiDimArrayTest.conversionToView 13: [ OK ] MultiDimArrayTest.conversionToView (0 ms) 13: [ RUN ] MultiDimArrayTest.conversionToConstView 13: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) 13: [ RUN ] MultiDimArrayTest.viewBegin 13: [ OK ] MultiDimArrayTest.viewBegin (0 ms) 13: [ RUN ] MultiDimArrayTest.viewEnd 13: [ OK ] MultiDimArrayTest.viewEnd (0 ms) 13: [ RUN ] MultiDimArrayTest.constViewConstBegin 13: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) 13: [ RUN ] MultiDimArrayTest.constViewConstEnd 13: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) 13: [----------] 25 tests from MultiDimArrayTest (1 ms total) 13: 13: [----------] 4 tests from MultiDimArrayToMdSpanTest 13: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan 13: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) 13: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan 13: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) 13: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan 13: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) 13: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan 13: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) 13: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/0, where TypeParam = std::allocator 13: [ RUN ] PaddedVectorTest/0.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/0.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/0.CanCopyAssign 13: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/0.CanMoveAssign 13: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/0.CanSwap 13: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/0 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/1, where TypeParam = std::allocator 13: [ RUN ] PaddedVectorTest/1.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/1.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/1.CanCopyAssign 13: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/1.CanMoveAssign 13: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/1.CanSwap 13: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/1 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/2, where TypeParam = std::allocator 13: [ RUN ] PaddedVectorTest/2.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/2.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/2.CanCopyAssign 13: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/2.CanMoveAssign 13: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/2.CanSwap 13: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/2 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 13: [ RUN ] PaddedVectorTest/3.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/3.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/3.CanCopyAssign 13: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/3.CanMoveAssign 13: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/3.CanSwap 13: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/3 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 13: [ RUN ] PaddedVectorTest/4.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/4.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/4.CanCopyAssign 13: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/4.CanMoveAssign 13: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/4.CanSwap 13: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/4 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 13: [ RUN ] PaddedVectorTest/5.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/5.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/5.CanCopyAssign 13: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/5.CanMoveAssign 13: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/5.CanSwap 13: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/5 (1 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 13: [ RUN ] PaddedVectorTest/6.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/6.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/6.CanCopyAssign 13: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/6.CanMoveAssign 13: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/6.CanSwap 13: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/6 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 13: [ RUN ] PaddedVectorTest/7.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/7.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/7.CanCopyAssign 13: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/7.CanMoveAssign 13: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/7.CanSwap 13: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/7 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 13: [ RUN ] PaddedVectorTest/8.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/8.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/8.CanCopyAssign 13: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/8.CanMoveAssign 13: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/8.CanSwap 13: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/8 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 13: [ RUN ] PaddedVectorTest/9.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/9.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/9.CanCopyAssign 13: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/9.CanMoveAssign 13: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/9.CanSwap 13: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/9 (0 ms total) 13: 13: [----------] 37 tests from RVecTest 13: [ RUN ] RVecTest.CanBeStoredInVector 13: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 13: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 13: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 13: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 13: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 13: [ RUN ] RVecTest.WorksAsMutable_rvec 13: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 13: [ RUN ] RVecTest.WorksAs_rvec_Array 13: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 13: [ RUN ] RVecTest.CanAddRVecToRvec 13: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 13: [ RUN ] RVecTest.CanAddAssignRVecToRvec 13: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 13: [ RUN ] RVecTest.CanSubtractRVecFromRvec 13: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 13: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 13: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 13: [ RUN ] RVecTest.CanDotProductRVecByRvec 13: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 13: [ RUN ] RVecTest.CanCrossProductRVecByRvec 13: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 13: [ RUN ] RVecTest.CanDivideRVecInplace 13: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 13: [ RUN ] RVecTest.CanScaleRVec 13: [ OK ] RVecTest.CanScaleRVec (0 ms) 13: [ RUN ] RVecTest.CanDivideRVec 13: [ OK ] RVecTest.CanDivideRVec (0 ms) 13: [ RUN ] RVecTest.CanDoUnitvFromRVec 13: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 13: [ RUN ] RVecTest.CanSqLengthOfRVec 13: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 13: [ RUN ] RVecTest.CanLengthOfRVec 13: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 13: [ RUN ] RVecTest.CanCastToRVec 13: [ OK ] RVecTest.CanCastToRVec (0 ms) 13: [ RUN ] RVecTest.CanCastToDVec 13: [ OK ] RVecTest.CanCastToDVec (0 ms) 13: [ RUN ] RVecTest.CanLeftScalarMultiply 13: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 13: [ RUN ] RVecTest.CanRightScalarMultiply 13: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 13: [ RUN ] RVecTest.CanGetUnitvFromRVec 13: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 13: [ RUN ] RVecTest.CanGetSqLengthOfRVec 13: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 13: [ RUN ] RVecTest.CanGetLengthOfRVec 13: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 13: [ RUN ] RVecTest.CanDoCrossProductOfRVec 13: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 13: [ RUN ] RVecTest.CanDoDotProductOfRVec 13: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 13: [ RUN ] RVecTest.CanScaleByVector 13: [ OK ] RVecTest.CanScaleByVector (0 ms) 13: [ RUN ] RVecTest.asIVec 13: [ OK ] RVecTest.asIVec (0 ms) 13: [ RUN ] RVecTest.elementWiseMin 13: [ OK ] RVecTest.elementWiseMin (0 ms) 13: [ RUN ] RVecTest.elementWiseMax 13: [ OK ] RVecTest.elementWiseMax (0 ms) 13: [ RUN ] RVecTest.WorksAs_dvec_Reference 13: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 13: [ RUN ] RVecTest.WorksAs_ivec_Reference 13: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 13: [ RUN ] RVecTest.WorksAs_rvec_Reference 13: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 13: [ RUN ] RVecTest.CopyConstructorWorks 13: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 13: [ RUN ] RVecTest.CopyAssignmentWorks 13: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 13: [ RUN ] RVecTest.MoveConstructorWorks 13: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 13: [ RUN ] RVecTest.MoveAssignmentWorks 13: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 13: [----------] 37 tests from RVecTest (1 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 204 tests from 29 test cases ran. (137 ms total) 13: [ PASSED ] 204 tests. 13/30 Test #13: MathUnitTests .................... Passed 0.17 sec test 14 Start 14: MdrunUtilityUnitTests 14: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/bin/mdrunutility-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/Testing/Temporary/MdrunUtilityUnitTests.xml" 14: Test timeout computed to be: 30 14: [==========] Running 17 tests from 1 test case. 14: [----------] Global test environment set-up. 14: [----------] 17 tests from ThreadAffinityTest 14: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 14: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 14: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 14: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (1 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 14: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 14: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 14: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 14: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) 14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 14: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 14: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (1 ms) 14: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 14: NOTE: Affinity setting failed. 14: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) 14: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 14: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (0 ms) 14: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 14: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (1 ms) 14: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 14: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (0 ms) 14: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 14: NOTE: Affinity setting for 1/2 threads failed. 14: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (0 ms) 14: [----------] 17 tests from ThreadAffinityTest (3 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 17 tests from 1 test case ran. (3 ms total) 14: [ PASSED ] 17 tests. 14/30 Test #14: MdrunUtilityUnitTests ............ Passed 0.03 sec test 15 Start 15: MdrunUtilityMpiUnitTests 15: Test command: /usr/bin/mpiexec.mpich "-np" "4" "-host" "localhost" "/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/bin/mdrunutility-mpi-test" "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 15: Test timeout computed to be: 30 15: [==========] Running 13 tests from 2 test cases. 15: [----------] Global test environment set-up. 15: [----------] 6 tests from ThreadAffinityMultiRankTest 15: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 15: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (0 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 15: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (1 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 15: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (3 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 15: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (0 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 15: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (0 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 15: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (0 ms) 15: [----------] 6 tests from ThreadAffinityMultiRankTest (5 ms total) 15: 15: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (1 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (4 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (1 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (0 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (0 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (1 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (1 ms) 15: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (9 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 13 tests from 2 test cases ran. (14 ms total) 15: [ PASSED ] 13 tests. 15/30 Test #15: MdrunUtilityMpiUnitTests ......... Passed 0.16 sec test 16 Start 16: MDSpanTests 16: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/bin/mdspan-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/Testing/Temporary/MDSpanTests.xml" 16: Test timeout computed to be: 30 16: [==========] Running 32 tests from 7 test cases. 16: [----------] Global test environment set-up. 16: [----------] 4 tests from BasicAccessorPolicy 16: [ RUN ] BasicAccessorPolicy.Decay 16: [ OK ] BasicAccessorPolicy.Decay (0 ms) 16: [ RUN ] BasicAccessorPolicy.Access 16: [ OK ] BasicAccessorPolicy.Access (0 ms) 16: [ RUN ] BasicAccessorPolicy.Offset 16: [ OK ] BasicAccessorPolicy.Offset (0 ms) 16: [ RUN ] BasicAccessorPolicy.CopyAccessor 16: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) 16: [----------] 4 tests from BasicAccessorPolicy (0 ms total) 16: 16: [----------] 4 tests from ExtentsTest 16: [ RUN ] ExtentsTest.Construction 16: [ OK ] ExtentsTest.Construction (0 ms) 16: [ RUN ] ExtentsTest.PurelyStatic 16: [ OK ] ExtentsTest.PurelyStatic (0 ms) 16: [ RUN ] ExtentsTest.RankNought 16: [ OK ] ExtentsTest.RankNought (0 ms) 16: [ RUN ] ExtentsTest.Assignment 16: [ OK ] ExtentsTest.Assignment (0 ms) 16: [----------] 4 tests from ExtentsTest (0 ms total) 16: 16: [----------] 8 tests from MdSpanExtension 16: [ RUN ] MdSpanExtension.SlicingAllStatic 16: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) 16: [ RUN ] MdSpanExtension.SlicingDynamic 16: [ OK ] MdSpanExtension.SlicingDynamic (0 ms) 16: [ RUN ] MdSpanExtension.SlicingAllStatic3D 16: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) 16: [ RUN ] MdSpanExtension.SlicingEqualsView3D 16: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) 16: [ RUN ] MdSpanExtension.additionWorks 16: [ OK ] MdSpanExtension.additionWorks (0 ms) 16: [ RUN ] MdSpanExtension.subtractionWorks 16: [ OK ] MdSpanExtension.subtractionWorks (0 ms) 16: [ RUN ] MdSpanExtension.multiplicationWorks 16: [ OK ] MdSpanExtension.multiplicationWorks (0 ms) 16: [ RUN ] MdSpanExtension.divisionWorks 16: [ OK ] MdSpanExtension.divisionWorks (0 ms) 16: [----------] 8 tests from MdSpanExtension (0 ms total) 16: 16: [----------] 3 tests from LayoutTests 16: [ RUN ] LayoutTests.LayoutRightConstruction 16: [ OK ] LayoutTests.LayoutRightConstruction (0 ms) 16: [ RUN ] LayoutTests.LayoutRightProperties 16: [ OK ] LayoutTests.LayoutRightProperties (0 ms) 16: [ RUN ] LayoutTests.LayoutRightOperator 16: [ OK ] LayoutTests.LayoutRightOperator (0 ms) 16: [----------] 3 tests from LayoutTests (0 ms total) 16: 16: [----------] 1 test from MdSpanTest 16: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly 16: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) 16: [----------] 1 test from MdSpanTest (0 ms total) 16: 16: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 16: [ RUN ] MdSpanTest/0.Rank 16: [ OK ] MdSpanTest/0.Rank (0 ms) 16: [ RUN ] MdSpanTest/0.DynamicRank 16: [ OK ] MdSpanTest/0.DynamicRank (0 ms) 16: [ RUN ] MdSpanTest/0.Extents 16: [ OK ] MdSpanTest/0.Extents (0 ms) 16: [ RUN ] MdSpanTest/0.Strides 16: [ OK ] MdSpanTest/0.Strides (0 ms) 16: [ RUN ] MdSpanTest/0.Properties 16: [ OK ] MdSpanTest/0.Properties (0 ms) 16: [ RUN ] MdSpanTest/0.Operator 16: [ OK ] MdSpanTest/0.Operator (0 ms) 16: [----------] 6 tests from MdSpanTest/0 (0 ms total) 16: 16: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 16: [ RUN ] MdSpanTest/1.Rank 16: [ OK ] MdSpanTest/1.Rank (0 ms) 16: [ RUN ] MdSpanTest/1.DynamicRank 16: [ OK ] MdSpanTest/1.DynamicRank (0 ms) 16: [ RUN ] MdSpanTest/1.Extents 16: [ OK ] MdSpanTest/1.Extents (0 ms) 16: [ RUN ] MdSpanTest/1.Strides 16: [ OK ] MdSpanTest/1.Strides (0 ms) 16: [ RUN ] MdSpanTest/1.Properties 16: [ OK ] MdSpanTest/1.Properties (0 ms) 16: [ RUN ] MdSpanTest/1.Operator 16: [ OK ] MdSpanTest/1.Operator (0 ms) 16: [----------] 6 tests from MdSpanTest/1 (0 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 32 tests from 7 test cases ran. (1 ms total) 16: [ PASSED ] 32 tests. 16/30 Test #16: MDSpanTests ...................... Passed 0.10 sec test 17 Start 17: OnlineHelpUnitTests 17: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/bin/onlinehelp-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/Testing/Temporary/OnlineHelpUnitTests.xml" 17: Test timeout computed to be: 30 17: [==========] Running 22 tests from 4 test cases. 17: [----------] Global test environment set-up. 17: [----------] 6 tests from TextTableFormatterTest 17: [ RUN ] TextTableFormatterTest.HandlesBasicCase 17: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms) 17: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 17: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) 17: [ RUN ] TextTableFormatterTest.HandlesIndentation 17: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) 17: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 17: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) 17: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 17: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms) 17: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 17: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) 17: [----------] 6 tests from TextTableFormatterTest (0 ms total) 17: 17: [----------] 3 tests from HelpManagerTest 17: [ RUN ] HelpManagerTest.HandlesRootTopic 17: [ OK ] HelpManagerTest.HandlesRootTopic (1 ms) 17: [ RUN ] HelpManagerTest.HandlesSubTopics 17: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 17: [ RUN ] HelpManagerTest.HandlesInvalidTopics 17: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 17: [----------] 3 tests from HelpManagerTest (1 ms total) 17: 17: [----------] 2 tests from HelpTopicFormattingTest 17: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 17: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms) 17: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 17: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) 17: [----------] 2 tests from HelpTopicFormattingTest (0 ms total) 17: 17: [----------] 11 tests from HelpWriterContextTest 17: [ RUN ] HelpWriterContextTest.FormatsParagraphs 17: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 17: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 17: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 17: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (1 ms) 17: [ RUN ] HelpWriterContextTest.FormatsLiteralText 17: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 17: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 17: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsBulletList 17: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 17: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 17: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsGridTable 17: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsTitles 17: [ OK ] HelpWriterContextTest.FormatsTitles (1 ms) 17: [----------] 11 tests from HelpWriterContextTest (2 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 22 tests from 4 test cases ran. (4 ms total) 17: [ PASSED ] 22 tests. 17/30 Test #17: OnlineHelpUnitTests .............. Passed 0.03 sec test 18 Start 18: OptionsUnitTests 18: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/bin/options-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/Testing/Temporary/OptionsUnitTests.xml" 18: Test timeout computed to be: 30 18: [==========] Running 110 tests from 18 test cases. 18: [----------] Global test environment set-up. 18: [----------] 5 tests from AbstractOptionStorageTest 18: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 18: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 18: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 18: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) 18: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 18: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 18: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 18: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 18: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 18: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 18: [----------] 5 tests from AbstractOptionStorageTest (0 ms total) 18: 18: [----------] 8 tests from FileNameOptionTest 18: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 18: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 18: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 18: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 18: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 18: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 18: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 18: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 18: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 18: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 18: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 18: [----------] 8 tests from FileNameOptionTest (0 ms total) 18: 18: [----------] 15 tests from FileNameOptionManagerTest 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 18: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 18: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 18: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 18: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 18: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 18: [----------] 15 tests from FileNameOptionManagerTest (1 ms total) 18: 18: [----------] 1 test from OptionsTest 18: [ RUN ] OptionsTest.FailsOnNonsafeStorage 18: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 18: [----------] 1 test from OptionsTest (0 ms total) 18: 18: [----------] 9 tests from OptionsAssignerTest 18: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 18: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 18: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 18: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 18: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesMissingValue 18: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesExtraValue 18: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesGroups 18: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesSections 18: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 18: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 18: [----------] 9 tests from OptionsAssignerTest (0 ms total) 18: 18: [----------] 4 tests from OptionsAssignerBooleanTest 18: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 18: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 18: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 18: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 18: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 18: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 18: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 18: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 18: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 18: 18: [----------] 13 tests from OptionsAssignerIntegerTest 18: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 18: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 18: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 18: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 18: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 18: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 18: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 18: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 18: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 18: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 18: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 18: [----------] 13 tests from OptionsAssignerIntegerTest (1 ms total) 18: 18: [----------] 5 tests from OptionsAssignerDoubleTest 18: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 18: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 18: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 18: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 18: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 18: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 18: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 18: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 18: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 18: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 18: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 18: 18: [----------] 9 tests from OptionsAssignerStringTest 18: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 18: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 18: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 18: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 18: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 18: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 18: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 18: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 18: 18: [----------] 6 tests from OptionsAssignerEnumTest 18: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 18: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 18: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 18: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 18: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 18: 18: [----------] 8 tests from RepeatingOptionSectionTest 18: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 18: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 18: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 18: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 18: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 18: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 18: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 18: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 18: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 18: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 18: 18: [----------] 1 test from TimeUnitManagerTest 18: [ RUN ] TimeUnitManagerTest.BasicOperations 18: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 18: [----------] 1 test from TimeUnitManagerTest (0 ms total) 18: 18: [----------] 4 tests from TimeUnitBehaviorTest 18: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 18: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 18: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 18: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 18: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 18: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 18: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 18: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 18: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 18: 18: [----------] 2 tests from TreeValueSupportAssignTest 18: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 18: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 18: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 18: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 18: [----------] 2 tests from TreeValueSupportAssignTest (1 ms total) 18: 18: [----------] 1 test from TreeValueSupportAssignErrorTest 18: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 18: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 18: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 18: 18: [----------] 5 tests from TreeValueSupportCheckTest 18: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 18: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 18: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 18: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 18: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 18: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 18: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 18: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 18: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 18: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 18: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 18: 18: [----------] 6 tests from TreeValueSupportAdjustTest 18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms) 18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) 18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms) 18: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 18: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 18: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 18: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) 18: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 18: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 18: [----------] 6 tests from TreeValueSupportAdjustTest (0 ms total) 18: 18: [----------] 8 tests from TreeValueSupportTest 18: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 18: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 18: [ OK ] TreeValueSupportTest.SupportsIntegerOption (1 ms) 18: [ RUN ] TreeValueSupportTest.SupportsInt64Option 18: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsStringOption 18: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsFloatOption 18: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 18: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsEnumIntOption 18: [ OK ] TreeValueSupportTest.SupportsEnumIntOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsEnumOption 18: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) 18: [----------] 8 tests from TreeValueSupportTest (1 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 110 tests from 18 test cases ran. (4 ms total) 18: [ PASSED ] 110 tests. 18/30 Test #18: OptionsUnitTests ................. Passed 0.02 sec test 19 Start 19: PbcutilUnitTest 19: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/bin/pbcutil-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/Testing/Temporary/PbcutilUnitTest.xml" 19: Test timeout computed to be: 30 19: [==========] Running 3 tests from 2 test cases. 19: [----------] Global test environment set-up. 19: [----------] 1 test from PbcTest 19: [ RUN ] PbcTest.CalcShiftsWorks 19: [ OK ] PbcTest.CalcShiftsWorks (1 ms) 19: [----------] 1 test from PbcTest (1 ms total) 19: 19: [----------] 2 tests from PbcEnumsTest 19: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect 19: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms) 19: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect 19: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) 19: [----------] 2 tests from PbcEnumsTest (0 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 3 tests from 2 test cases ran. (1 ms total) 19: [ PASSED ] 3 tests. 19/30 Test #19: PbcutilUnitTest .................. Passed 0.06 sec test 20 Start 20: RandomUnitTests 20: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/bin/random-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/Testing/Temporary/RandomUnitTests.xml" 20: Test timeout computed to be: 30 20: [==========] Running 44 tests from 10 test cases. 20: [----------] Global test environment set-up. 20: [----------] 4 tests from ExponentialDistributionTest 20: [ RUN ] ExponentialDistributionTest.Output 20: [ OK ] ExponentialDistributionTest.Output (0 ms) 20: [ RUN ] ExponentialDistributionTest.Logical 20: [ OK ] ExponentialDistributionTest.Logical (0 ms) 20: [ RUN ] ExponentialDistributionTest.Reset 20: [ OK ] ExponentialDistributionTest.Reset (0 ms) 20: [ RUN ] ExponentialDistributionTest.AltParam 20: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 20: [----------] 4 tests from ExponentialDistributionTest (0 ms total) 20: 20: [----------] 4 tests from GammaDistributionTest 20: [ RUN ] GammaDistributionTest.Output 20: [ OK ] GammaDistributionTest.Output (0 ms) 20: [ RUN ] GammaDistributionTest.Logical 20: [ OK ] GammaDistributionTest.Logical (0 ms) 20: [ RUN ] GammaDistributionTest.Reset 20: [ OK ] GammaDistributionTest.Reset (0 ms) 20: [ RUN ] GammaDistributionTest.AltParam 20: [ OK ] GammaDistributionTest.AltParam (0 ms) 20: [----------] 4 tests from GammaDistributionTest (0 ms total) 20: 20: [----------] 4 tests from NormalDistributionTest 20: [ RUN ] NormalDistributionTest.Output 20: [ OK ] NormalDistributionTest.Output (1 ms) 20: [ RUN ] NormalDistributionTest.Logical 20: [ OK ] NormalDistributionTest.Logical (0 ms) 20: [ RUN ] NormalDistributionTest.Reset 20: [ OK ] NormalDistributionTest.Reset (0 ms) 20: [ RUN ] NormalDistributionTest.AltParam 20: [ OK ] NormalDistributionTest.AltParam (0 ms) 20: [----------] 4 tests from NormalDistributionTest (1 ms total) 20: 20: [----------] 1 test from SeedTest 20: [ RUN ] SeedTest.makeRandomSeed 20: [ OK ] SeedTest.makeRandomSeed (0 ms) 20: [----------] 1 test from SeedTest (0 ms total) 20: 20: [----------] 6 tests from TabulatedNormalDistributionTest 20: [ RUN ] TabulatedNormalDistributionTest.Output14 20: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) 20: [ RUN ] TabulatedNormalDistributionTest.Output16 20: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) 20: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 20: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) 20: [ RUN ] TabulatedNormalDistributionTest.Logical 20: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 20: [ RUN ] TabulatedNormalDistributionTest.Reset 20: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 20: [ RUN ] TabulatedNormalDistributionTest.AltParam 20: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 20: [----------] 6 tests from TabulatedNormalDistributionTest (0 ms total) 20: 20: [----------] 1 test from TabulatedNormalDistributionTableTest 20: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 20: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (2 ms) 20: [----------] 1 test from TabulatedNormalDistributionTableTest (2 ms total) 20: 20: [----------] 6 tests from ThreeFry2x64Test 20: [ RUN ] ThreeFry2x64Test.Logical 20: [ OK ] ThreeFry2x64Test.Logical (0 ms) 20: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 20: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) 20: [ RUN ] ThreeFry2x64Test.Reseed 20: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 20: [ RUN ] ThreeFry2x64Test.Discard 20: [ OK ] ThreeFry2x64Test.Discard (0 ms) 20: [ RUN ] ThreeFry2x64Test.InvalidCounter 20: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 20: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 20: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 20: [----------] 6 tests from ThreeFry2x64Test (0 ms total) 20: 20: [----------] 4 tests from UniformIntDistributionTest 20: [ RUN ] UniformIntDistributionTest.Output 20: [ OK ] UniformIntDistributionTest.Output (0 ms) 20: [ RUN ] UniformIntDistributionTest.Logical 20: [ OK ] UniformIntDistributionTest.Logical (0 ms) 20: [ RUN ] UniformIntDistributionTest.Reset 20: [ OK ] UniformIntDistributionTest.Reset (0 ms) 20: [ RUN ] UniformIntDistributionTest.AltParam 20: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 20: [----------] 4 tests from UniformIntDistributionTest (0 ms total) 20: 20: [----------] 5 tests from UniformRealDistributionTest 20: [ RUN ] UniformRealDistributionTest.GenerateCanonical 20: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 20: [ RUN ] UniformRealDistributionTest.Output 20: [ OK ] UniformRealDistributionTest.Output (0 ms) 20: [ RUN ] UniformRealDistributionTest.Logical 20: [ OK ] UniformRealDistributionTest.Logical (0 ms) 20: [ RUN ] UniformRealDistributionTest.Reset 20: [ OK ] UniformRealDistributionTest.Reset (0 ms) 20: [ RUN ] UniformRealDistributionTest.AltParam 20: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 20: [----------] 5 tests from UniformRealDistributionTest (1 ms total) 20: 20: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 20: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (0 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 44 tests from 10 test cases ran. (4 ms total) 20: [ PASSED ] 44 tests. 20/30 Test #20: RandomUnitTests .................. Passed 0.04 sec test 21 Start 21: RestraintTests 21: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/bin/restraintpotential-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/Testing/Temporary/RestraintTests.xml" 21: Test timeout computed to be: 30 21: [==========] Running 1 test from 1 test case. 21: [----------] Global test environment set-up. 21: [----------] 1 test from RestraintManager 21: [ RUN ] RestraintManager.restraintList 21: [ OK ] RestraintManager.restraintList (0 ms) 21: [----------] 1 test from RestraintManager (0 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 1 test from 1 test case ran. (0 ms total) 21: [ PASSED ] 1 test. 21/30 Test #21: RestraintTests ................... Passed 0.05 sec test 22 Start 22: TableUnitTests 22: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/bin/table-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/Testing/Temporary/TableUnitTests.xml" 22: Test timeout computed to be: 30 22: [==========] Running 20 tests from 2 test cases. 22: [----------] Global test environment set-up. 22: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 22: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 22: [ OK ] SplineTableTest/0.HandlesIncorrectInput (1 ms) 22: [ RUN ] SplineTableTest/0.Sinc 22: [ OK ] SplineTableTest/0.Sinc (1 ms) 22: [ RUN ] SplineTableTest/0.LJ12 22: [ OK ] SplineTableTest/0.LJ12 (12 ms) 22: [ RUN ] SplineTableTest/0.PmeCorrection 22: [ OK ] SplineTableTest/0.PmeCorrection (1 ms) 22: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 22: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (0 ms) 22: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 22: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (1 ms) 22: [ RUN ] SplineTableTest/0.TwoFunctions 22: [ OK ] SplineTableTest/0.TwoFunctions (21 ms) 22: [ RUN ] SplineTableTest/0.ThreeFunctions 22: [ OK ] SplineTableTest/0.ThreeFunctions (48 ms) 22: [ RUN ] SplineTableTest/0.Simd 22: [ OK ] SplineTableTest/0.Simd (6 ms) 22: [ RUN ] SplineTableTest/0.SimdTwoFunctions 22: [ OK ] SplineTableTest/0.SimdTwoFunctions (21 ms) 22: [----------] 10 tests from SplineTableTest/0 (112 ms total) 22: 22: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 22: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 22: [ OK ] SplineTableTest/1.HandlesIncorrectInput (1 ms) 22: [ RUN ] SplineTableTest/1.Sinc 22: [ OK ] SplineTableTest/1.Sinc (0 ms) 22: [ RUN ] SplineTableTest/1.LJ12 22: [ OK ] SplineTableTest/1.LJ12 (2 ms) 22: [ RUN ] SplineTableTest/1.PmeCorrection 22: [ OK ] SplineTableTest/1.PmeCorrection (1 ms) 22: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 22: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms) 22: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 22: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (1 ms) 22: [ RUN ] SplineTableTest/1.TwoFunctions 22: [ OK ] SplineTableTest/1.TwoFunctions (4 ms) 22: [ RUN ] SplineTableTest/1.ThreeFunctions 22: [ OK ] SplineTableTest/1.ThreeFunctions (3 ms) 22: [ RUN ] SplineTableTest/1.Simd 22: [ OK ] SplineTableTest/1.Simd (1 ms) 22: [ RUN ] SplineTableTest/1.SimdTwoFunctions 22: [ OK ] SplineTableTest/1.SimdTwoFunctions (3 ms) 22: [----------] 10 tests from SplineTableTest/1 (16 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 20 tests from 2 test cases ran. (129 ms total) 22: [ PASSED ] 20 tests. 22/30 Test #22: TableUnitTests ................... Passed 0.15 sec test 23 Start 23: TaskAssignmentUnitTests 23: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/bin/taskassignment-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/Testing/Temporary/TaskAssignmentUnitTests.xml" 23: Test timeout computed to be: 30 23: [==========] Running 3 tests from 2 test cases. 23: [----------] Global test environment set-up. 23: [----------] 2 tests from UserTaskAssignmentStringHandlingTest 23: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork 23: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms) 23: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid 23: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) 23: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total) 23: 23: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest 23: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow 23: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (0 ms) 23: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (0 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 3 tests from 2 test cases ran. (0 ms total) 23: [ PASSED ] 3 tests. 23/30 Test #23: TaskAssignmentUnitTests .......... Passed 0.04 sec test 24 Start 24: TopologyTest 24: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/bin/topology-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/Testing/Temporary/TopologyTest.xml" 24: Test timeout computed to be: 30 24: [==========] Running 11 tests from 3 test cases. 24: [----------] Global test environment set-up. 24: [----------] 3 tests from ExclusionBlockTest 24: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks 24: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) 24: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka 24: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) 24: [ RUN ] ExclusionBlockTest.MergeExclusions 24: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) 24: [----------] 3 tests from ExclusionBlockTest (0 ms total) 24: 24: [----------] 2 tests from MtopTest 24: [ RUN ] MtopTest.RangeBasedLoop 24: [ OK ] MtopTest.RangeBasedLoop (0 ms) 24: [ RUN ] MtopTest.Operators 24: [ OK ] MtopTest.Operators (0 ms) 24: [----------] 2 tests from MtopTest (1 ms total) 24: 24: [----------] 6 tests from SymtabTest 24: [ RUN ] SymtabTest.EmptyOnOpen 24: [ OK ] SymtabTest.EmptyOnOpen (0 ms) 24: [ RUN ] SymtabTest.AddSingleEntry 24: [ OK ] SymtabTest.AddSingleEntry (0 ms) 24: [ RUN ] SymtabTest.AddTwoDistinctEntries 24: [ OK ] SymtabTest.AddTwoDistinctEntries (0 ms) 24: [ RUN ] SymtabTest.TryToAddDuplicates 24: [ OK ] SymtabTest.TryToAddDuplicates (0 ms) 24: [ RUN ] SymtabTest.AddLargeNumberOfEntries 24: [ OK ] SymtabTest.AddLargeNumberOfEntries (0 ms) 24: [ RUN ] SymtabTest.NoDuplicatesInLargeTable 24: [ OK ] SymtabTest.NoDuplicatesInLargeTable (0 ms) 24: [----------] 6 tests from SymtabTest (0 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 11 tests from 3 test cases ran. (1 ms total) 24: [ PASSED ] 11 tests. 24/30 Test #24: TopologyTest ..................... Passed 0.02 sec test 25 Start 25: PullTest 25: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/bin/pull-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/Testing/Temporary/PullTest.xml" 25: Test timeout computed to be: 30 25: [==========] Running 5 tests from 1 test case. 25: [----------] Global test environment set-up. 25: [----------] 5 tests from PullTest 25: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 25: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 25: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 25: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 25: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 25: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 25: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 25: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 25: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 25: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 25: [----------] 5 tests from PullTest (0 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 5 tests from 1 test case ran. (0 ms total) 25: [ PASSED ] 5 tests. 25/30 Test #25: PullTest ......................... Passed 0.02 sec test 26 Start 26: AwhTest 26: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/bin/awh-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/Testing/Temporary/AwhTest.xml" 26: Test timeout computed to be: 30 26: [==========] Running 12 tests from 4 test cases. 26: [----------] Global test environment set-up. 26: [----------] 1 test from BiasTest 26: [ RUN ] BiasTest.DetectsCovering 26: [ OK ] BiasTest.DetectsCovering (0 ms) 26: [----------] 1 test from BiasTest (0 ms total) 26: 26: [----------] 1 test from gridTest 26: [ RUN ] gridTest.neighborhood 26: [ OK ] gridTest.neighborhood (1 ms) 26: [----------] 1 test from gridTest (1 ms total) 26: 26: [----------] 8 tests from WithParameters/BiasTest 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (1 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (0 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (1 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (0 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (0 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (1 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (0 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (0 ms) 26: [----------] 8 tests from WithParameters/BiasTest (3 ms total) 26: 26: [----------] 2 tests from WithParameters/BiasStateTest 26: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 26: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (1 ms) 26: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 26: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms) 26: [----------] 2 tests from WithParameters/BiasStateTest (1 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 12 tests from 4 test cases ran. (5 ms total) 26: [ PASSED ] 12 tests. 26/30 Test #26: AwhTest .......................... Passed 0.02 sec test 27 Start 27: SimdUnitTests 27: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/bin/simd-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/Testing/Temporary/SimdUnitTests.xml" 27: Test timeout computed to be: 30 27: [==========] Running 288 tests from 22 test cases. 27: [----------] Global test environment set-up. 27: [----------] 9 tests from SimdBootstrapTest 27: [ RUN ] SimdBootstrapTest.loadStore 27: [ OK ] SimdBootstrapTest.loadStore (0 ms) 27: [ RUN ] SimdBootstrapTest.loadU 27: [ OK ] SimdBootstrapTest.loadU (0 ms) 27: [ RUN ] SimdBootstrapTest.storeU 27: [ OK ] SimdBootstrapTest.storeU (0 ms) 27: [ RUN ] SimdBootstrapTest.loadStoreI 27: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) 27: [ RUN ] SimdBootstrapTest.loadUI 27: [ OK ] SimdBootstrapTest.loadUI (0 ms) 27: [ RUN ] SimdBootstrapTest.storeUI 27: [ OK ] SimdBootstrapTest.storeUI (0 ms) 27: [ RUN ] SimdBootstrapTest.simd4LoadStore 27: [ OK ] SimdBootstrapTest.simd4LoadStore (0 ms) 27: [ RUN ] SimdBootstrapTest.simd4LoadU 27: [ OK ] SimdBootstrapTest.simd4LoadU (0 ms) 27: [ RUN ] SimdBootstrapTest.simd4StoreU 27: [ OK ] SimdBootstrapTest.simd4StoreU (0 ms) 27: [----------] 9 tests from SimdBootstrapTest (0 ms total) 27: 27: [----------] 1 test from SimdTest 27: [ RUN ] SimdTest.GmxAligned 27: [ OK ] SimdTest.GmxAligned (0 ms) 27: [----------] 1 test from SimdTest (0 ms total) 27: 27: [----------] 42 tests from SimdFloatingpointTest 27: [ RUN ] SimdFloatingpointTest.setZero 27: [ OK ] SimdFloatingpointTest.setZero (0 ms) 27: [ RUN ] SimdFloatingpointTest.set 27: [ OK ] SimdFloatingpointTest.set (0 ms) 27: [ RUN ] SimdFloatingpointTest.add 27: [ OK ] SimdFloatingpointTest.add (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskAdd 27: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) 27: [ RUN ] SimdFloatingpointTest.sub 27: [ OK ] SimdFloatingpointTest.sub (0 ms) 27: [ RUN ] SimdFloatingpointTest.mul 27: [ OK ] SimdFloatingpointTest.mul (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskzMul 27: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) 27: [ RUN ] SimdFloatingpointTest.fma 27: [ OK ] SimdFloatingpointTest.fma (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskzFma 27: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) 27: [ RUN ] SimdFloatingpointTest.fms 27: [ OK ] SimdFloatingpointTest.fms (0 ms) 27: [ RUN ] SimdFloatingpointTest.fnma 27: [ OK ] SimdFloatingpointTest.fnma (0 ms) 27: [ RUN ] SimdFloatingpointTest.fnms 27: [ OK ] SimdFloatingpointTest.fnms (0 ms) 27: [ RUN ] SimdFloatingpointTest.abs 27: [ OK ] SimdFloatingpointTest.abs (0 ms) 27: [ RUN ] SimdFloatingpointTest.neg 27: [ OK ] SimdFloatingpointTest.neg (0 ms) 27: [ RUN ] SimdFloatingpointTest.and 27: [ OK ] SimdFloatingpointTest.and (0 ms) 27: [ RUN ] SimdFloatingpointTest.or 27: [ OK ] SimdFloatingpointTest.or (0 ms) 27: [ RUN ] SimdFloatingpointTest.xor 27: [ OK ] SimdFloatingpointTest.xor (0 ms) 27: [ RUN ] SimdFloatingpointTest.andNot 27: [ OK ] SimdFloatingpointTest.andNot (0 ms) 27: [ RUN ] SimdFloatingpointTest.max 27: [ OK ] SimdFloatingpointTest.max (0 ms) 27: [ RUN ] SimdFloatingpointTest.min 27: [ OK ] SimdFloatingpointTest.min (0 ms) 27: [ RUN ] SimdFloatingpointTest.round 27: [ OK ] SimdFloatingpointTest.round (0 ms) 27: [ RUN ] SimdFloatingpointTest.roundMode 27: [ OK ] SimdFloatingpointTest.roundMode (0 ms) 27: [ RUN ] SimdFloatingpointTest.trunc 27: [ OK ] SimdFloatingpointTest.trunc (0 ms) 27: [ RUN ] SimdFloatingpointTest.frexp 27: [ OK ] SimdFloatingpointTest.frexp (0 ms) 27: [ RUN ] SimdFloatingpointTest.ldexp 27: [ OK ] SimdFloatingpointTest.ldexp (0 ms) 27: [ RUN ] SimdFloatingpointTest.rsqrt 27: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskzRsqrt 27: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) 27: [ RUN ] SimdFloatingpointTest.rcp 27: [ OK ] SimdFloatingpointTest.rcp (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskzRcp 27: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) 27: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask 27: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) 27: [ RUN ] SimdFloatingpointTest.selectByNotMask 27: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) 27: [ RUN ] SimdFloatingpointTest.cmpNe 27: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) 27: [ RUN ] SimdFloatingpointTest.cmpLe 27: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) 27: [ RUN ] SimdFloatingpointTest.cmpLt 27: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) 27: [ RUN ] SimdFloatingpointTest.testBits 27: [ OK ] SimdFloatingpointTest.testBits (0 ms) 27: [ RUN ] SimdFloatingpointTest.andB 27: [ OK ] SimdFloatingpointTest.andB (0 ms) 27: [ RUN ] SimdFloatingpointTest.orB 27: [ OK ] SimdFloatingpointTest.orB (0 ms) 27: [ RUN ] SimdFloatingpointTest.anyTrueB 27: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) 27: [ RUN ] SimdFloatingpointTest.blend 27: [ OK ] SimdFloatingpointTest.blend (0 ms) 27: [ RUN ] SimdFloatingpointTest.reduce 27: [ OK ] SimdFloatingpointTest.reduce (0 ms) 27: [ RUN ] SimdFloatingpointTest.cvtFloat2Double 27: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) 27: [ RUN ] SimdFloatingpointTest.cvtDouble2Float 27: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) 27: [----------] 42 tests from SimdFloatingpointTest (0 ms total) 27: 27: [----------] 16 tests from SimdFloatingpointUtilTest 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets 27: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum 27: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.loadUNDuplicate4 27: [ OK ] SimdFloatingpointUtilTest.loadUNDuplicate4 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.load4DuplicateN 27: [ OK ] SimdFloatingpointUtilTest.load4DuplicateN (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.loadU4NOffset 27: [ OK ] SimdFloatingpointUtilTest.loadU4NOffset (0 ms) 27: [----------] 16 tests from SimdFloatingpointUtilTest (1 ms total) 27: 27: [----------] 3 tests from SimdVectorOperationsTest 27: [ RUN ] SimdVectorOperationsTest.iprod 27: [ OK ] SimdVectorOperationsTest.iprod (0 ms) 27: [ RUN ] SimdVectorOperationsTest.norm2 27: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) 27: [ RUN ] SimdVectorOperationsTest.cprod 27: [ OK ] SimdVectorOperationsTest.cprod (0 ms) 27: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) 27: 27: [----------] 56 tests from SimdMathTest 27: [ RUN ] SimdMathTest.generateTestPointsFloat 27: [ OK ] SimdMathTest.generateTestPointsFloat (0 ms) 27: [ RUN ] SimdMathTest.copysign 27: [ OK ] SimdMathTest.copysign (0 ms) 27: [ RUN ] SimdMathTest.invsqrt 27: [ OK ] SimdMathTest.invsqrt (1 ms) 27: [ RUN ] SimdMathTest.maskzInvsqrt 27: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) 27: [ RUN ] SimdMathTest.invsqrtPair 27: [ OK ] SimdMathTest.invsqrtPair (1 ms) 27: [ RUN ] SimdMathTest.sqrt 27: [ OK ] SimdMathTest.sqrt (1 ms) 27: [ RUN ] SimdMathTest.sqrtUnsafe 27: [ OK ] SimdMathTest.sqrtUnsafe (1 ms) 27: [ RUN ] SimdMathTest.inv 27: [ OK ] SimdMathTest.inv (3 ms) 27: [ RUN ] SimdMathTest.maskzInv 27: [ OK ] SimdMathTest.maskzInv (0 ms) 27: [ RUN ] SimdMathTest.cbrt 27: [ OK ] SimdMathTest.cbrt (1 ms) 27: [ RUN ] SimdMathTest.invcbrt 27: [ OK ] SimdMathTest.invcbrt (3 ms) 27: [ RUN ] SimdMathTest.log2 27: [ OK ] SimdMathTest.log2 (0 ms) 27: [ RUN ] SimdMathTest.log 27: [ OK ] SimdMathTest.log (1 ms) 27: [ RUN ] SimdMathTest.exp2 27: [ OK ] SimdMathTest.exp2 (1 ms) 27: [ RUN ] SimdMathTest.exp2Unsafe 27: [ OK ] SimdMathTest.exp2Unsafe (1 ms) 27: [ RUN ] SimdMathTest.exp 27: [ OK ] SimdMathTest.exp (1 ms) 27: [ RUN ] SimdMathTest.expUnsafe 27: [ OK ] SimdMathTest.expUnsafe (1 ms) 27: [ RUN ] SimdMathTest.pow 27: [ OK ] SimdMathTest.pow (0 ms) 27: [ RUN ] SimdMathTest.powUnsafe 27: [ OK ] SimdMathTest.powUnsafe (0 ms) 27: [ RUN ] SimdMathTest.erf 27: [ OK ] SimdMathTest.erf (1 ms) 27: [ RUN ] SimdMathTest.erfc 27: [ OK ] SimdMathTest.erfc (1 ms) 27: [ RUN ] SimdMathTest.sin 27: [ OK ] SimdMathTest.sin (1 ms) 27: [ RUN ] SimdMathTest.cos 27: [ OK ] SimdMathTest.cos (1 ms) 27: [ RUN ] SimdMathTest.tan 27: [ OK ] SimdMathTest.tan (1 ms) 27: [ RUN ] SimdMathTest.asin 27: [ OK ] SimdMathTest.asin (0 ms) 27: [ RUN ] SimdMathTest.acos 27: [ OK ] SimdMathTest.acos (0 ms) 27: [ RUN ] SimdMathTest.atan 27: [ OK ] SimdMathTest.atan (0 ms) 27: [ RUN ] SimdMathTest.atan2 27: [ OK ] SimdMathTest.atan2 (0 ms) 27: [ RUN ] SimdMathTest.pmeForceCorrection 27: [ OK ] SimdMathTest.pmeForceCorrection (1 ms) 27: [ RUN ] SimdMathTest.pmePotentialCorrection 27: [ OK ] SimdMathTest.pmePotentialCorrection (1 ms) 27: [ RUN ] SimdMathTest.invsqrtSingleAccuracy 27: [ OK ] SimdMathTest.invsqrtSingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy 27: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.sqrtSingleAccuracy 27: [ OK ] SimdMathTest.sqrtSingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe 27: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (0 ms) 27: [ RUN ] SimdMathTest.invSingleAccuracy 27: [ OK ] SimdMathTest.invSingleAccuracy (3 ms) 27: [ RUN ] SimdMathTest.cbrtSingleAccuracy 27: [ OK ] SimdMathTest.cbrtSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.invcbrtSingleAccuracy 27: [ OK ] SimdMathTest.invcbrtSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.log2SingleAccuracy 27: [ OK ] SimdMathTest.log2SingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.logSingleAccuracy 27: [ OK ] SimdMathTest.logSingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.exp2SingleAccuracy 27: [ OK ] SimdMathTest.exp2SingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 27: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (0 ms) 27: [ RUN ] SimdMathTest.expSingleAccuracy 27: [ OK ] SimdMathTest.expSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe 27: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (0 ms) 27: [ RUN ] SimdMathTest.powSingleAccuracy 27: [ OK ] SimdMathTest.powSingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.powSingleAccuracyUnsafe 27: [ OK ] SimdMathTest.powSingleAccuracyUnsafe (0 ms) 27: [ RUN ] SimdMathTest.erfSingleAccuracy 27: [ OK ] SimdMathTest.erfSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.erfcSingleAccuracy 27: [ OK ] SimdMathTest.erfcSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.sinSingleAccuracy 27: [ OK ] SimdMathTest.sinSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.cosSingleAccuracy 27: [ OK ] SimdMathTest.cosSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.tanSingleAccuracy 27: [ OK ] SimdMathTest.tanSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.asinSingleAccuracy 27: [ OK ] SimdMathTest.asinSingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.acosSingleAccuracy 27: [ OK ] SimdMathTest.acosSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.atanSingleAccuracy 27: [ OK ] SimdMathTest.atanSingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.atan2SingleAccuracy 27: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy 27: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 27: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (1 ms) 27: [----------] 56 tests from SimdMathTest (43 ms total) 27: 27: [----------] 1 test from EmptyArrayRefTest 27: [ RUN ] EmptyArrayRefTest.IsEmpty 27: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 27: [----------] 1 test from EmptyArrayRefTest (0 ms total) 27: 27: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 27: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 27: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks 27: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) 27: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks 27: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) 27: [----------] 3 tests from ArrayRefTest/0 (0 ms total) 27: 27: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 27: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 27: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks 27: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) 27: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks 27: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) 27: [----------] 3 tests from ArrayRefTest/1 (0 ms total) 27: 27: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 27: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 27: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks 27: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) 27: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks 27: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) 27: [----------] 3 tests from ArrayRefTest/2 (0 ms total) 27: 27: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 27: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 27: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks 27: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) 27: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks 27: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) 27: [----------] 3 tests from ArrayRefTest/3 (0 ms total) 27: 27: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefReadWriteTest/0.Assignment 27: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) 27: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) 27: 27: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefReadWriteTest/1.Assignment 27: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) 27: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) 27: 27: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefArithmeticTest/0.Basic 27: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) 27: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) 27: 27: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefArithmeticTest/1.Basic 27: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) 27: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) 27: 27: [----------] 23 tests from SimdIntegerTest 27: [ RUN ] SimdIntegerTest.setZero 27: [ OK ] SimdIntegerTest.setZero (0 ms) 27: [ RUN ] SimdIntegerTest.set 27: [ OK ] SimdIntegerTest.set (0 ms) 27: [ RUN ] SimdIntegerTest.add 27: [ OK ] SimdIntegerTest.add (0 ms) 27: [ RUN ] SimdIntegerTest.sub 27: [ OK ] SimdIntegerTest.sub (0 ms) 27: [ RUN ] SimdIntegerTest.mul 27: [ OK ] SimdIntegerTest.mul (0 ms) 27: [ RUN ] SimdIntegerTest.and 27: [ OK ] SimdIntegerTest.and (0 ms) 27: [ RUN ] SimdIntegerTest.andNot 27: [ OK ] SimdIntegerTest.andNot (0 ms) 27: [ RUN ] SimdIntegerTest.or 27: [ OK ] SimdIntegerTest.or (0 ms) 27: [ RUN ] SimdIntegerTest.xor 27: [ OK ] SimdIntegerTest.xor (0 ms) 27: [ RUN ] SimdIntegerTest.extract 27: [ OK ] SimdIntegerTest.extract (0 ms) 27: [ RUN ] SimdIntegerTest.cvtR2I 27: [ OK ] SimdIntegerTest.cvtR2I (0 ms) 27: [ RUN ] SimdIntegerTest.cvttR2I 27: [ OK ] SimdIntegerTest.cvttR2I (0 ms) 27: [ RUN ] SimdIntegerTest.cvtI2R 27: [ OK ] SimdIntegerTest.cvtI2R (0 ms) 27: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask 27: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) 27: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask 27: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) 27: [ RUN ] SimdIntegerTest.cmpLt 27: [ OK ] SimdIntegerTest.cmpLt (0 ms) 27: [ RUN ] SimdIntegerTest.testBits 27: [ OK ] SimdIntegerTest.testBits (0 ms) 27: [ RUN ] SimdIntegerTest.andB 27: [ OK ] SimdIntegerTest.andB (0 ms) 27: [ RUN ] SimdIntegerTest.orB 27: [ OK ] SimdIntegerTest.orB (0 ms) 27: [ RUN ] SimdIntegerTest.anyTrue 27: [ OK ] SimdIntegerTest.anyTrue (0 ms) 27: [ RUN ] SimdIntegerTest.blend 27: [ OK ] SimdIntegerTest.blend (0 ms) 27: [ RUN ] SimdIntegerTest.cvtB2IB 27: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) 27: [ RUN ] SimdIntegerTest.cvtIB2B 27: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) 27: [----------] 23 tests from SimdIntegerTest (0 ms total) 27: 27: [----------] 32 tests from Simd4FloatingpointTest 27: [ RUN ] Simd4FloatingpointTest.setZero 27: [ OK ] Simd4FloatingpointTest.setZero (0 ms) 27: [ RUN ] Simd4FloatingpointTest.set 27: [ OK ] Simd4FloatingpointTest.set (0 ms) 27: [ RUN ] Simd4FloatingpointTest.add 27: [ OK ] Simd4FloatingpointTest.add (0 ms) 27: [ RUN ] Simd4FloatingpointTest.sub 27: [ OK ] Simd4FloatingpointTest.sub (0 ms) 27: [ RUN ] Simd4FloatingpointTest.mul 27: [ OK ] Simd4FloatingpointTest.mul (0 ms) 27: [ RUN ] Simd4FloatingpointTest.fma 27: [ OK ] Simd4FloatingpointTest.fma (0 ms) 27: [ RUN ] Simd4FloatingpointTest.fms 27: [ OK ] Simd4FloatingpointTest.fms (0 ms) 27: [ RUN ] Simd4FloatingpointTest.fnma 27: [ OK ] Simd4FloatingpointTest.fnma (0 ms) 27: [ RUN ] Simd4FloatingpointTest.fnms 27: [ OK ] Simd4FloatingpointTest.fnms (0 ms) 27: [ RUN ] Simd4FloatingpointTest.abs 27: [ OK ] Simd4FloatingpointTest.abs (0 ms) 27: [ RUN ] Simd4FloatingpointTest.neg 27: [ OK ] Simd4FloatingpointTest.neg (0 ms) 27: [ RUN ] Simd4FloatingpointTest.and 27: [ OK ] Simd4FloatingpointTest.and (0 ms) 27: [ RUN ] Simd4FloatingpointTest.or 27: [ OK ] Simd4FloatingpointTest.or (0 ms) 27: [ RUN ] Simd4FloatingpointTest.xor 27: [ OK ] Simd4FloatingpointTest.xor (0 ms) 27: [ RUN ] Simd4FloatingpointTest.andNot 27: [ OK ] Simd4FloatingpointTest.andNot (0 ms) 27: [ RUN ] Simd4FloatingpointTest.max 27: [ OK ] Simd4FloatingpointTest.max (0 ms) 27: [ RUN ] Simd4FloatingpointTest.min 27: [ OK ] Simd4FloatingpointTest.min (0 ms) 27: [ RUN ] Simd4FloatingpointTest.round 27: [ OK ] Simd4FloatingpointTest.round (0 ms) 27: [ RUN ] Simd4FloatingpointTest.trunc 27: [ OK ] Simd4FloatingpointTest.trunc (0 ms) 27: [ RUN ] Simd4FloatingpointTest.gmxSimd4RsqrtR 27: [ OK ] Simd4FloatingpointTest.gmxSimd4RsqrtR (0 ms) 27: [ RUN ] Simd4FloatingpointTest.cmpEqAndSelectByMask 27: [ OK ] Simd4FloatingpointTest.cmpEqAndSelectByMask (0 ms) 27: [ RUN ] Simd4FloatingpointTest.selectByNotMask 27: [ OK ] Simd4FloatingpointTest.selectByNotMask (0 ms) 27: [ RUN ] Simd4FloatingpointTest.cmpNe 27: [ OK ] Simd4FloatingpointTest.cmpNe (0 ms) 27: [ RUN ] Simd4FloatingpointTest.cmpLe 27: [ OK ] Simd4FloatingpointTest.cmpLe (0 ms) 27: [ RUN ] Simd4FloatingpointTest.cmpLt 27: [ OK ] Simd4FloatingpointTest.cmpLt (0 ms) 27: [ RUN ] Simd4FloatingpointTest.andB 27: [ OK ] Simd4FloatingpointTest.andB (0 ms) 27: [ RUN ] Simd4FloatingpointTest.orB 27: [ OK ] Simd4FloatingpointTest.orB (0 ms) 27: [ RUN ] Simd4FloatingpointTest.anyTrue 27: [ OK ] Simd4FloatingpointTest.anyTrue (0 ms) 27: [ RUN ] Simd4FloatingpointTest.blend 27: [ OK ] Simd4FloatingpointTest.blend (0 ms) 27: [ RUN ] Simd4FloatingpointTest.reduce 27: [ OK ] Simd4FloatingpointTest.reduce (0 ms) 27: [ RUN ] Simd4FloatingpointTest.dotProduct 27: [ OK ] Simd4FloatingpointTest.dotProduct (0 ms) 27: [ RUN ] Simd4FloatingpointTest.transpose 27: [ OK ] Simd4FloatingpointTest.transpose (0 ms) 27: [----------] 32 tests from Simd4FloatingpointTest (0 ms total) 27: 27: [----------] 1 test from Simd4VectorOperationsTest 27: [ RUN ] Simd4VectorOperationsTest.norm2 27: [ OK ] Simd4VectorOperationsTest.norm2 (0 ms) 27: [----------] 1 test from Simd4VectorOperationsTest (0 ms total) 27: 27: [----------] 2 tests from Simd4MathTest 27: [ RUN ] Simd4MathTest.invsqrt 27: [ OK ] Simd4MathTest.invsqrt (0 ms) 27: [ RUN ] Simd4MathTest.invsqrtSingleAccuracy 27: [ OK ] Simd4MathTest.invsqrtSingleAccuracy (0 ms) 27: [----------] 2 tests from Simd4MathTest (0 ms total) 27: 27: [----------] 41 tests from SimdScalarTest 27: [ RUN ] SimdScalarTest.load 27: [ OK ] SimdScalarTest.load (0 ms) 27: [ RUN ] SimdScalarTest.loadU 27: [ OK ] SimdScalarTest.loadU (0 ms) 27: [ RUN ] SimdScalarTest.store 27: [ OK ] SimdScalarTest.store (0 ms) 27: [ RUN ] SimdScalarTest.storeU 27: [ OK ] SimdScalarTest.storeU (0 ms) 27: [ RUN ] SimdScalarTest.setZero 27: [ OK ] SimdScalarTest.setZero (0 ms) 27: [ RUN ] SimdScalarTest.andNot 27: [ OK ] SimdScalarTest.andNot (0 ms) 27: [ RUN ] SimdScalarTest.fma 27: [ OK ] SimdScalarTest.fma (0 ms) 27: [ RUN ] SimdScalarTest.fms 27: [ OK ] SimdScalarTest.fms (0 ms) 27: [ RUN ] SimdScalarTest.fnma 27: [ OK ] SimdScalarTest.fnma (0 ms) 27: [ RUN ] SimdScalarTest.fnms 27: [ OK ] SimdScalarTest.fnms (0 ms) 27: [ RUN ] SimdScalarTest.maskAdd 27: [ OK ] SimdScalarTest.maskAdd (0 ms) 27: [ RUN ] SimdScalarTest.maskzMul 27: [ OK ] SimdScalarTest.maskzMul (0 ms) 27: [ RUN ] SimdScalarTest.maskzFma 27: [ OK ] SimdScalarTest.maskzFma (0 ms) 27: [ RUN ] SimdScalarTest.abs 27: [ OK ] SimdScalarTest.abs (0 ms) 27: [ RUN ] SimdScalarTest.max 27: [ OK ] SimdScalarTest.max (0 ms) 27: [ RUN ] SimdScalarTest.min 27: [ OK ] SimdScalarTest.min (0 ms) 27: [ RUN ] SimdScalarTest.round 27: [ OK ] SimdScalarTest.round (0 ms) 27: [ RUN ] SimdScalarTest.trunc 27: [ OK ] SimdScalarTest.trunc (0 ms) 27: [ RUN ] SimdScalarTest.reduce 27: [ OK ] SimdScalarTest.reduce (0 ms) 27: [ RUN ] SimdScalarTest.testBits 27: [ OK ] SimdScalarTest.testBits (0 ms) 27: [ RUN ] SimdScalarTest.anyTrue 27: [ OK ] SimdScalarTest.anyTrue (0 ms) 27: [ RUN ] SimdScalarTest.selectByMask 27: [ OK ] SimdScalarTest.selectByMask (0 ms) 27: [ RUN ] SimdScalarTest.selectByNotMask 27: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 27: [ RUN ] SimdScalarTest.blend 27: [ OK ] SimdScalarTest.blend (0 ms) 27: [ RUN ] SimdScalarTest.cvtR2I 27: [ OK ] SimdScalarTest.cvtR2I (0 ms) 27: [ RUN ] SimdScalarTest.cvttR2I 27: [ OK ] SimdScalarTest.cvttR2I (0 ms) 27: [ RUN ] SimdScalarTest.cvtI2R 27: [ OK ] SimdScalarTest.cvtI2R (0 ms) 27: [ RUN ] SimdScalarTest.cvtF2D 27: [ OK ] SimdScalarTest.cvtF2D (0 ms) 27: [ RUN ] SimdScalarTest.cvtD2D 27: [ OK ] SimdScalarTest.cvtD2D (0 ms) 27: [ RUN ] SimdScalarTest.loadI 27: [ OK ] SimdScalarTest.loadI (0 ms) 27: [ RUN ] SimdScalarTest.loadUI 27: [ OK ] SimdScalarTest.loadUI (0 ms) 27: [ RUN ] SimdScalarTest.storeI 27: [ OK ] SimdScalarTest.storeI (0 ms) 27: [ RUN ] SimdScalarTest.storeUI 27: [ OK ] SimdScalarTest.storeUI (0 ms) 27: [ RUN ] SimdScalarTest.andNotI 27: [ OK ] SimdScalarTest.andNotI (0 ms) 27: [ RUN ] SimdScalarTest.testBitsI 27: [ OK ] SimdScalarTest.testBitsI (0 ms) 27: [ RUN ] SimdScalarTest.selectByMaskI 27: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 27: [ RUN ] SimdScalarTest.selectByNotMaskI 27: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 27: [ RUN ] SimdScalarTest.blendI 27: [ OK ] SimdScalarTest.blendI (0 ms) 27: [ RUN ] SimdScalarTest.cvtB2IB 27: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 27: [ RUN ] SimdScalarTest.cvtIB2B 27: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 27: [ RUN ] SimdScalarTest.expandScalarsToTriplets 27: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 27: [----------] 41 tests from SimdScalarTest (1 ms total) 27: 27: [----------] 8 tests from SimdScalarUtilTest 27: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 27: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 27: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 27: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 27: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 27: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 27: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 27: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 27: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 27: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 27: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 27: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 27: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 27: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 27: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 27: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 27: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 27: 27: [----------] 37 tests from SimdScalarMathTest 27: [ RUN ] SimdScalarMathTest.copysign 27: [ OK ] SimdScalarMathTest.copysign (0 ms) 27: [ RUN ] SimdScalarMathTest.invsqrtPair 27: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 27: [ RUN ] SimdScalarMathTest.inv 27: [ OK ] SimdScalarMathTest.inv (0 ms) 27: [ RUN ] SimdScalarMathTest.maskzInvsqrt 27: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 27: [ RUN ] SimdScalarMathTest.log 27: [ OK ] SimdScalarMathTest.log (0 ms) 27: [ RUN ] SimdScalarMathTest.exp2 27: [ OK ] SimdScalarMathTest.exp2 (0 ms) 27: [ RUN ] SimdScalarMathTest.exp 27: [ OK ] SimdScalarMathTest.exp (0 ms) 27: [ RUN ] SimdScalarMathTest.erf 27: [ OK ] SimdScalarMathTest.erf (0 ms) 27: [ RUN ] SimdScalarMathTest.erfc 27: [ OK ] SimdScalarMathTest.erfc (0 ms) 27: [ RUN ] SimdScalarMathTest.sincos 27: [ OK ] SimdScalarMathTest.sincos (0 ms) 27: [ RUN ] SimdScalarMathTest.sin 27: [ OK ] SimdScalarMathTest.sin (0 ms) 27: [ RUN ] SimdScalarMathTest.cos 27: [ OK ] SimdScalarMathTest.cos (0 ms) 27: [ RUN ] SimdScalarMathTest.tan 27: [ OK ] SimdScalarMathTest.tan (0 ms) 27: [ RUN ] SimdScalarMathTest.asin 27: [ OK ] SimdScalarMathTest.asin (0 ms) 27: [ RUN ] SimdScalarMathTest.acos 27: [ OK ] SimdScalarMathTest.acos (0 ms) 27: [ RUN ] SimdScalarMathTest.atan 27: [ OK ] SimdScalarMathTest.atan (0 ms) 27: [ RUN ] SimdScalarMathTest.atan2 27: [ OK ] SimdScalarMathTest.atan2 (0 ms) 27: [ RUN ] SimdScalarMathTest.pmeForceCorrection 27: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 27: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 27: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 27: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 27: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.invSingleAccuracy 27: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 27: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.logSingleAccuracy 27: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 27: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.expSingleAccuracy 27: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 27: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 27: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 27: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 27: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 27: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 27: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 27: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 27: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 27: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 27: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 27: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 27: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 27: [----------] 37 tests from SimdScalarMathTest (0 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 288 tests from 22 test cases ran. (46 ms total) 27: [ PASSED ] 288 tests. 27/30 Test #27: SimdUnitTests .................... Passed 0.14 sec test 28 Start 28: CompatibilityHelpersTests 28: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/bin/compat-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/Testing/Temporary/CompatibilityHelpersTests.xml" 28: Test timeout computed to be: 30 28: [==========] Running 170 tests from 12 test cases. 28: [----------] Global test environment set-up. 28: [----------] 45 tests from OptionalTest 28: [ RUN ] OptionalTest.UnionCanContainNonPodTypes 28: [ OK ] OptionalTest.UnionCanContainNonPodTypes (0 ms) 28: [ RUN ] OptionalTest.CanDefaultConstructEmpty 28: [ OK ] OptionalTest.CanDefaultConstructEmpty (0 ms) 28: [ RUN ] OptionalTest.CanConstructFromNullopt 28: [ OK ] OptionalTest.CanConstructFromNullopt (0 ms) 28: [ RUN ] OptionalTest.CanDefaultConstructUsingNonDefaultConstructibleType 28: [ OK ] OptionalTest.CanDefaultConstructUsingNonDefaultConstructibleType (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptional 28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptional (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptional 28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptional (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptionalWithExplicitConversion 28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptionalWithExplicitConversion (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptionalNonExplicitConverting 28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptionalNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptionalExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptionalExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptionalNonExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptionalNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptional 28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptional (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptionalExplicitConverting 28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptionalExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptionalNonExplicitConverting 28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptionalNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptional 28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptional (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptionalExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptionalExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptionalNonExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptionalNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromLiteral 28: [ OK ] OptionalTest.CanCopyConstructFromLiteral (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromLiteralConverting 28: [ OK ] OptionalTest.CanCopyConstructFromLiteralConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromValue 28: [ OK ] OptionalTest.CanCopyConstructFromValue (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromValueConverting 28: [ OK ] OptionalTest.CanCopyConstructFromValueConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromValue 28: [ OK ] OptionalTest.CanMoveConstructFromValue (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromValueExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromValueExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromValueNonExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromValueNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceConstructFromLiteral 28: [ OK ] OptionalTest.CanInPlaceConstructFromLiteral (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceCopyConstructFromValue 28: [ OK ] OptionalTest.CanInPlaceCopyConstructFromValue (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceMoveConstructFromValue 28: [ OK ] OptionalTest.CanInPlaceMoveConstructFromValue (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceCopyConstructFromInitializerList 28: [ OK ] OptionalTest.CanInPlaceCopyConstructFromInitializerList (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceMoveConstructFromInitializerList 28: [ OK ] OptionalTest.CanInPlaceMoveConstructFromInitializerList (0 ms) 28: [ RUN ] OptionalTest.CanAssignNulloptToDisengage 28: [ OK ] OptionalTest.CanAssignNulloptToDisengage (0 ms) 28: [ RUN ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionals 28: [ OK ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionals (0 ms) 28: [ RUN ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionalsConverting 28: [ OK ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionalsConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionalsConverting 28: [ OK ] OptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionalsConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyAssignFromLiteral 28: [ OK ] OptionalTest.CanCopyAssignFromLiteral (0 ms) 28: [ RUN ] OptionalTest.CanCopyAssignFromValue 28: [ OK ] OptionalTest.CanCopyAssignFromValue (0 ms) 28: [ RUN ] OptionalTest.CanMoveAssignFromValue 28: [ OK ] OptionalTest.CanMoveAssignFromValue (0 ms) 28: [ RUN ] OptionalTest.CanCopyEmplaceFromArguments 28: [ OK ] OptionalTest.CanCopyEmplaceFromArguments (0 ms) 28: [ RUN ] OptionalTest.CanMoveEmplaceFromArguments 28: [ OK ] OptionalTest.CanMoveEmplaceFromArguments (0 ms) 28: [ RUN ] OptionalTest.CanCopyEmplaceFromInitializerListAndArguments 28: [ OK ] OptionalTest.CanCopyEmplaceFromInitializerListAndArguments (0 ms) 28: [ RUN ] OptionalTest.CanMoveEmplaceFromInitializerListAndArguments 28: [ OK ] OptionalTest.CanMoveEmplaceFromInitializerListAndArguments (0 ms) 28: [ RUN ] OptionalTest.CanResetContent 28: [ OK ] OptionalTest.CanResetContent (0 ms) 28: [ RUN ] OptionalTest.ProvidesRelationalOperators 28: [ OK ] OptionalTest.ProvidesRelationalOperators (0 ms) 28: [ RUN ] OptionalTest.ProvidesMixedTypeRelationalOperators 28: [ OK ] OptionalTest.ProvidesMixedTypeRelationalOperators (0 ms) 28: [ RUN ] OptionalTest.CanProduceHash 28: [ OK ] OptionalTest.CanProduceHash (1 ms) 28: [ RUN ] OptionalTest.ShowAlignmentDependingOnBaseType 28: alignment_of: 1 28: alignment_of: 2 28: alignment_of: 4 28: alignment_of: 8 28: alignment_of: 4 28: alignment_of: 8 28: alignment_of: 16 28: alignment_of: 1 28: [ OK ] OptionalTest.ShowAlignmentDependingOnBaseType (0 ms) 28: [ RUN ] OptionalTest.ShowSizeDependingOnBaseType 28: sizeof( nonstd::optional_lite::detail::storage_t ): 1 28: sizeof( optional ): 2 (1) 28: sizeof( optional ): 4 (2) 28: sizeof( optional ): 8 (4) 28: sizeof( optional ): 16 (8) 28: sizeof( optional ): 8 (4) 28: sizeof( optional ): 16 (8) 28: sizeof( optional ): 32 (16) 28: sizeof( optional ): 2 (1) 28: [ OK ] OptionalTest.ShowSizeDependingOnBaseType (0 ms) 28: [----------] 45 tests from OptionalTest (2 ms total) 28: 28: [----------] 7 tests from MakeOptionalTest 28: [ RUN ] MakeOptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionals 28: [ OK ] MakeOptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionals (0 ms) 28: [ RUN ] MakeOptionalTest.CanCopyConstruct 28: [ OK ] MakeOptionalTest.CanCopyConstruct (0 ms) 28: [ RUN ] MakeOptionalTest.CanMoveConstruct 28: [ OK ] MakeOptionalTest.CanMoveConstruct (0 ms) 28: [ RUN ] MakeOptionalTest.CanInPlaceCopyConstructFromArguments 28: [ OK ] MakeOptionalTest.CanInPlaceCopyConstructFromArguments (0 ms) 28: [ RUN ] MakeOptionalTest.CanInPlaceMoveConstructFromArguments 28: [ OK ] MakeOptionalTest.CanInPlaceMoveConstructFromArguments (0 ms) 28: [ RUN ] MakeOptionalTest.CanInPlaceCopyConstructFromInitializerListAndArguments 28: [ OK ] MakeOptionalTest.CanInPlaceCopyConstructFromInitializerListAndArguments (0 ms) 28: [ RUN ] MakeOptionalTest.CanInPlaceMoveConstructFromInitializerListAndArguments 28: [ OK ] MakeOptionalTest.CanInPlaceMoveConstructFromInitializerListAndArguments (0 ms) 28: [----------] 7 tests from MakeOptionalTest (0 ms total) 28: 28: [----------] 4 tests from OptionalMemberSwapTest 28: [ RUN ] OptionalMemberSwapTest.CanSwapDisengagedWithDisengaged 28: [ OK ] OptionalMemberSwapTest.CanSwapDisengagedWithDisengaged (0 ms) 28: [ RUN ] OptionalMemberSwapTest.CanSwapEngagedWithDisengaged 28: [ OK ] OptionalMemberSwapTest.CanSwapEngagedWithDisengaged (0 ms) 28: [ RUN ] OptionalMemberSwapTest.CanSwapDisengagedWithEngaged 28: [ OK ] OptionalMemberSwapTest.CanSwapDisengagedWithEngaged (0 ms) 28: [ RUN ] OptionalMemberSwapTest.CanSwapEngagedWithEngaged 28: [ OK ] OptionalMemberSwapTest.CanSwapEngagedWithEngaged (0 ms) 28: [----------] 4 tests from OptionalMemberSwapTest (0 ms total) 28: 28: [----------] 4 tests from OptionalImplicitValueTest 28: [ RUN ] OptionalImplicitValueTest.CanObtainValueConst 28: [ OK ] OptionalImplicitValueTest.CanObtainValueConst (0 ms) 28: [ RUN ] OptionalImplicitValueTest.CanObtainValueNonConst 28: [ OK ] OptionalImplicitValueTest.CanObtainValueNonConst (0 ms) 28: [ RUN ] OptionalImplicitValueTest.CanObtainMovedFromValueConst 28: [ OK ] OptionalImplicitValueTest.CanObtainMovedFromValueConst (0 ms) 28: [ RUN ] OptionalImplicitValueTest.CanObtainMovedFromValueNonConst 28: [ OK ] OptionalImplicitValueTest.CanObtainMovedFromValueNonConst (0 ms) 28: [----------] 4 tests from OptionalImplicitValueTest (0 ms total) 28: 28: [----------] 20 tests from OptionalIntValueTest 28: [ RUN ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorConst 28: [ OK ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorNonConst 28: [ OK ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorNonConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorConst 28: [ OK ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorNonConst 28: [ OK ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorNonConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainHasValueViaOperatorBool 28: [ OK ] OptionalIntValueTest.CanObtainHasValueViaOperatorBool (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainValueViaValueMethodConst 28: [ OK ] OptionalIntValueTest.CanObtainValueViaValueMethodConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainValueViaValueMethodNonConst 28: [ OK ] OptionalIntValueTest.CanObtainValueViaValueMethodNonConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodConst 28: [ OK ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodNonConst 28: [ OK ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodNonConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainValueFromNonEmptyOptionalViaValueOrMethod 28: [ OK ] OptionalIntValueTest.CanObtainValueFromNonEmptyOptionalViaValueOrMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainDefaultFromEmptyOptionalViaValueOrMethod 28: [ OK ] OptionalIntValueTest.CanObtainDefaultFromEmptyOptionalViaValueOrMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedFromValueForLValuesViaValueOrMethod 28: [ OK ] OptionalIntValueTest.CanObtainMovedFromValueForLValuesViaValueOrMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedFromValueForRValuesViaValueOrMethod 28: [ OK ] OptionalIntValueTest.CanObtainMovedFromValueForRValuesViaValueOrMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForLValues 28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForLValues (1 ms) 28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForRValues 28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForRValues (0 ms) 28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessWithNonEmptyWhatMethod 28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessWithNonEmptyWhatMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithDisengaged 28: [ OK ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithDisengaged (0 ms) 28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithEngaged 28: [ OK ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithEngaged (0 ms) 28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithEngaged 28: [ OK ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithEngaged (0 ms) 28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithDisengaged 28: [ OK ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithDisengaged (0 ms) 28: [----------] 20 tests from OptionalIntValueTest (1 ms total) 28: 28: [----------] 1 test from NotNullConstruction 28: [ RUN ] NotNullConstruction.Works 28: [ OK ] NotNullConstruction.Works (0 ms) 28: [----------] 1 test from NotNullConstruction (0 ms total) 28: 28: [----------] 1 test from NotNullCasting 28: [ RUN ] NotNullCasting.Works 28: [ OK ] NotNullCasting.Works (0 ms) 28: [----------] 1 test from NotNullCasting (0 ms total) 28: 28: [----------] 1 test from NotNullAssignment 28: [ RUN ] NotNullAssignment.Works 28: [ OK ] NotNullAssignment.Works (0 ms) 28: [----------] 1 test from NotNullAssignment (0 ms total) 28: 28: [----------] 1 test from MakeNotNull 28: [ RUN ] MakeNotNull.Works 28: [ OK ] MakeNotNull.Works (0 ms) 28: [----------] 1 test from MakeNotNull (0 ms total) 28: 28: [----------] 1 test from NotNull 28: [ RUN ] NotNull.WorksInContainers 28: [ OK ] NotNull.WorksInContainers (0 ms) 28: [----------] 1 test from NotNull (0 ms total) 28: 28: [----------] 80 tests from StringViewTest 28: [ RUN ] StringViewTest.CanDefaultConstructEmptyView 28: [ OK ] StringViewTest.CanDefaultConstructEmptyView (0 ms) 28: [ RUN ] StringViewTest.CanConstructFromPointerAndSize 28: [ OK ] StringViewTest.CanConstructFromPointerAndSize (0 ms) 28: [ RUN ] StringViewTest.CanConstructFromCString 28: [ OK ] StringViewTest.CanConstructFromCString (0 ms) 28: [ RUN ] StringViewTest.CanCopyConstructFromEmptyView 28: [ OK ] StringViewTest.CanCopyConstructFromEmptyView (0 ms) 28: [ RUN ] StringViewTest.CanCopyConstructFromNonEmptyView 28: [ OK ] StringViewTest.CanCopyConstructFromNonEmptyView (0 ms) 28: [ RUN ] StringViewTest.CanCopyAssingFromEmptyView 28: [ OK ] StringViewTest.CanCopyAssingFromEmptyView (0 ms) 28: [ RUN ] StringViewTest.CanCopyAssingFromNonEmptyView 28: [ OK ] StringViewTest.CanCopyAssingFromNonEmptyView (0 ms) 28: [ RUN ] StringViewTest.AllowForwardIteration 28: [ OK ] StringViewTest.AllowForwardIteration (0 ms) 28: [ RUN ] StringViewTest.AllowConstForwardIteration 28: [ OK ] StringViewTest.AllowConstForwardIteration (0 ms) 28: [ RUN ] StringViewTest.AllowReverseIteration 28: [ OK ] StringViewTest.AllowReverseIteration (0 ms) 28: [ RUN ] StringViewTest.AllowConstReverseIteration 28: [ OK ] StringViewTest.AllowConstReverseIteration (0 ms) 28: [ RUN ] StringViewTest.CanObtainSizeFromViewViaSize 28: [ OK ] StringViewTest.CanObtainSizeFromViewViaSize (0 ms) 28: [ RUN ] StringViewTest.CanObtainSizeFromViewViaLength 28: [ OK ] StringViewTest.CanObtainSizeFromViewViaLength (0 ms) 28: [ RUN ] StringViewTest.CanObtainMaxSizeViaMaxSize 28: [ OK ] StringViewTest.CanObtainMaxSizeViaMaxSize (0 ms) 28: [ RUN ] StringViewTest.CanCheckForEmptyStringWithEmpty 28: [ OK ] StringViewTest.CanCheckForEmptyStringWithEmpty (0 ms) 28: [ RUN ] StringViewTest.CanAccessElementViaArrayIndex 28: [ OK ] StringViewTest.CanAccessElementViaArrayIndex (0 ms) 28: [ RUN ] StringViewTest.CanAccessElementViaAt 28: [ OK ] StringViewTest.CanAccessElementViaAt (0 ms) 28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsAccess 28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsAccess (0 ms) 28: [ RUN ] StringViewTest.CanAccessAllElementsViaData 28: [ OK ] StringViewTest.CanAccessAllElementsViaData (0 ms) 28: [ RUN ] StringViewTest.DataFromEmptyStringIsNullptr 28: [ OK ] StringViewTest.DataFromEmptyStringIsNullptr (0 ms) 28: [ RUN ] StringViewTest.CanRemovePrefix 28: [ OK ] StringViewTest.CanRemovePrefix (0 ms) 28: [ RUN ] StringViewTest.CanRemoveSuffix 28: [ OK ] StringViewTest.CanRemoveSuffix (0 ms) 28: [ RUN ] StringViewTest.CanSwapWithOtherView 28: [ OK ] StringViewTest.CanSwapWithOtherView (0 ms) 28: [ RUN ] StringViewTest.CanCopySubstringWithCopy 28: [ OK ] StringViewTest.CanCopySubstringWithCopy (0 ms) 28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsCopy 28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsCopy (0 ms) 28: [ RUN ] StringViewTest.CanObtainSubstringWithSubstr 28: [ OK ] StringViewTest.CanObtainSubstringWithSubstr (0 ms) 28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsSubstr 28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsSubstr (0 ms) 28: [ RUN ] StringViewTest.CanLexicallyCompareViewWithCompare 28: [ OK ] StringViewTest.CanLexicallyCompareViewWithCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareEmptyViewsWIthCompare 28: [ OK ] StringViewTest.CanCompareEmptyViewsWIthCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareSubStringWithViewViaCompare 28: [ OK ] StringViewTest.CanCompareSubStringWithViewViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareSubStringWithSubStringViewViaCompare 28: [ OK ] StringViewTest.CanCompareSubStringWithSubStringViewViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareToCStringViaCompare 28: [ OK ] StringViewTest.CanCompareToCStringViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareSubStringToCStringViaCompare 28: [ OK ] StringViewTest.CanCompareSubStringToCStringViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareSubStringToCStringPrefixViaCompare 28: [ OK ] StringViewTest.CanCompareSubStringToCStringPrefixViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCheckForPrefixViewViaStartsWith 28: [ OK ] StringViewTest.CanCheckForPrefixViewViaStartsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForPrefixCharacterViaStartsWith 28: [ OK ] StringViewTest.CanCheckForPrefixCharacterViaStartsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForPrefixCStringViaStartsWith 28: [ OK ] StringViewTest.CanCheckForPrefixCStringViaStartsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForSuffixViewViaEndsWith 28: [ OK ] StringViewTest.CanCheckForSuffixViewViaEndsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForSuffixCharacterViaEndsWith 28: [ OK ] StringViewTest.CanCheckForSuffixCharacterViaEndsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForSuffixCStringViaEndsWith 28: [ OK ] StringViewTest.CanCheckForSuffixCStringViaEndsWith (0 ms) 28: [ RUN ] StringViewTest.CanSearchForViewSubstrViaFind 28: [ OK ] StringViewTest.CanSearchForViewSubstrViaFind (0 ms) 28: [ RUN ] StringViewTest.CanSearchForCharacterViaFind 28: [ OK ] StringViewTest.CanSearchForCharacterViaFind (0 ms) 28: [ RUN ] StringViewTest.CanSearchForCStringSubstringViaFind 28: [ OK ] StringViewTest.CanSearchForCStringSubstringViaFind (0 ms) 28: [ RUN ] StringViewTest.CanSearchForCStringSubstringViaFindWithDefaultPos 28: [ OK ] StringViewTest.CanSearchForCStringSubstringViaFindWithDefaultPos (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForViewSubstrViaFind 28: [ OK ] StringViewTest.CanBackwardsSearchForViewSubstrViaFind (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForCharacterViaFind 28: [ OK ] StringViewTest.CanBackwardsSearchForCharacterViaFind (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFind 28: [ OK ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFind (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFindWithDefaultPos 28: [ OK ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFindWithDefaultPos (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfAnyCharacterInView 28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfAnyCharacterInView (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharacter 28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharacter (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCStringInLenght 28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCStringInLenght (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCString 28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCString (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfAnyCharacterInView 28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfAnyCharacterInView (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharacter 28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharacter (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCStringInLenght 28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCStringInLenght (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCString 28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCString (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstNotFoundCharacter 28: [ OK ] StringViewTest.CanSearchForFirstNotFoundCharacter (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstNonMatchingCharacter 28: [ OK ] StringViewTest.CanSearchForFirstNonMatchingCharacter (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCStringInLength 28: [ OK ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCStringInLength (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCString 28: [ OK ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCString (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForForstNonFoundCharacterInView 28: [ OK ] StringViewTest.CanBackwardsSearchForForstNonFoundCharacterInView (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonMatchingCharacter 28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonMatchingCharacter (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCStringInLength 28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCStringInLength (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCString 28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCString (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSV 28: [ OK ] StringViewTest.CanCreateViewWithLiteralSV (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsStringViewLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsStringViewLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInStringViewLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInStringViewLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SV 28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SV (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsStringViewLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsStringViewLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInStringViewLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInStringViewLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCompareToViews 28: [ OK ] StringViewTest.CanCompareToViews (0 ms) 28: [ RUN ] StringViewTest.CanCompareViewToImplicitlyConvertedView 28: [ OK ] StringViewTest.CanCompareViewToImplicitlyConvertedView (0 ms) 28: [ RUN ] StringViewTest.EmptyViewsCompareAsEqual 28: [ OK ] StringViewTest.EmptyViewsCompareAsEqual (0 ms) 28: [ RUN ] StringViewTest.CanPrintViewToPutputStream 28: [ OK ] StringViewTest.CanPrintViewToPutputStream (0 ms) 28: [ RUN ] StringViewTest.HashOfViewIsEqualToHashOfString 28: [ OK ] StringViewTest.HashOfViewIsEqualToHashOfString (0 ms) 28: [ RUN ] StringViewTest.HashOfWStringViewIsEqualToHashOfString 28: [ OK ] StringViewTest.HashOfWStringViewIsEqualToHashOfString (0 ms) 28: [ RUN ] StringViewTest.HashOfU16StringViewIsEqualToHashOfString 28: [ OK ] StringViewTest.HashOfU16StringViewIsEqualToHashOfString (0 ms) 28: [ RUN ] StringViewTest.HashOfU32StringViewIsEqualToHashOfString 28: [ OK ] StringViewTest.HashOfU32StringViewIsEqualToHashOfString (0 ms) 28: [----------] 80 tests from StringViewTest (2 ms total) 28: 28: [----------] 5 tests from StringViewExtensionTest 28: [ RUN ] StringViewExtensionTest.CanConstructViewFromString 28: [ OK ] StringViewExtensionTest.CanConstructViewFromString (0 ms) 28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaExplicitOperator 28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaExplicitOperator (0 ms) 28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaToString 28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaToString (0 ms) 28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaToStringFreeFunction 28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaToStringFreeFunction (0 ms) 28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViewViaToStringView 28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViewViaToStringView (0 ms) 28: [----------] 5 tests from StringViewExtensionTest (0 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 170 tests from 12 test cases ran. (5 ms total) 28: [ PASSED ] 170 tests. 28/30 Test #28: CompatibilityHelpersTests ........ Passed 0.03 sec test 29 Start 29: FileIOTests 29: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/bin/fileio-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/Testing/Temporary/FileIOTests.xml" 29: Test timeout computed to be: 30 29: [==========] Running 33 tests from 8 test cases. 29: [----------] Global test environment set-up. 29: [----------] 2 tests from FileMD5Test 29: [ RUN ] FileMD5Test.CanComputeMD5 29: [ OK ] FileMD5Test.CanComputeMD5 (2 ms) 29: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 29: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 29: [----------] 2 tests from FileMD5Test (2 ms total) 29: 29: [----------] 3 tests from MrcSerializer 29: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet 29: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) 29: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize 29: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms) 29: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip 29: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (1 ms) 29: [----------] 3 tests from MrcSerializer (1 ms total) 29: 29: [----------] 4 tests from MrcDensityMap 29: [ RUN ] MrcDensityMap.RoundTripIsIdempotent 29: [ OK ] MrcDensityMap.RoundTripIsIdempotent (0 ms) 29: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent 29: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (1 ms) 29: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile 29: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms) 29: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile 29: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (1 ms) 29: [----------] 4 tests from MrcDensityMap (2 ms total) 29: 29: [----------] 8 tests from MrcDensityMapHeaderTest 29: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader 29: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) 29: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect 29: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) 29: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid 29: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms) 29: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven 29: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) 29: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined 29: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms) 29: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues 29: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) 29: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents 29: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) 29: [ RUN ] MrcDensityMapHeaderTest.IsSane 29: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) 29: [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total) 29: 29: [----------] 9 tests from ReadTest 29: [ RUN ] ReadTest.get_eint_ReadsInteger 29: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 29: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 29: 29: ERROR 1 [file unknown, line 0]: 29: Right hand side '0.8' for parameter 'test' in parameter file is not an 29: integer value 29: 29: 29: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 29: [ RUN ] ReadTest.get_eint_WarnsAboutString 29: 29: ERROR 1 [file unknown, line 0]: 29: Right hand side 'hello' for parameter 'test' in parameter file is not an 29: integer value 29: 29: 29: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 29: [ RUN ] ReadTest.get_eint64_ReadsInteger 29: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 29: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 29: 29: ERROR 1 [file unknown, line 0]: 29: Right hand side '0.8' for parameter 'test' in parameter file is not an 29: integer value 29: 29: 29: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 29: [ RUN ] ReadTest.get_eint64_WarnsAboutString 29: 29: ERROR 1 [file unknown, line 0]: 29: Right hand side 'hello' for parameter 'test' in parameter file is not an 29: integer value 29: 29: 29: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 29: [ RUN ] ReadTest.get_ereal_ReadsInteger 29: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 29: [ RUN ] ReadTest.get_ereal_ReadsFloat 29: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 29: [ RUN ] ReadTest.get_ereal_WarnsAboutString 29: 29: ERROR 1 [file unknown, line 0]: 29: Right hand side 'hello' for parameter 'test' in parameter file is not a 29: real value 29: 29: 29: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 29: [----------] 9 tests from ReadTest (0 ms total) 29: 29: [----------] 1 test from FileIOXdrSerializerTest 29: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect 29: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (0 ms) 29: [----------] 1 test from FileIOXdrSerializerTest (0 ms total) 29: 29: [----------] 2 tests from TngTest 29: [ RUN ] TngTest.CanOpenTngFile 29: TNG library: Cannot open file spc2-traj.tng. ./src/external/tng_io/src/lib/tng_io.c: 890 29: TNG library: Cannot open file spc2-traj.tng. ./src/external/tng_io/src/lib/tng_io.c: 890 29: [ OK ] TngTest.CanOpenTngFile (1 ms) 29: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 29: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 29: [----------] 2 tests from TngTest (1 ms total) 29: 29: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 29: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 29: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (0 ms) 29: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 29: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (1 ms) 29: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 29: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (4 ms) 29: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 29: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (2 ms) 29: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (9 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 33 tests from 8 test cases ran. (15 ms total) 29: [ PASSED ] 33 tests. 29/30 Test #29: FileIOTests ...................... Passed 0.04 sec test 30 Start 30: SelectionUnitTests 30: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/bin/selection-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/Testing/Temporary/SelectionUnitTests.xml" 30: Test timeout computed to be: 30 30: [==========] Running 192 tests from 11 test cases. 30: [----------] Global test environment set-up. 30: [----------] 1 test from IndexGroupTest 30: [ RUN ] IndexGroupTest.RemovesDuplicates 30: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 30: [----------] 1 test from IndexGroupTest (0 ms total) 30: 30: [----------] 15 tests from IndexBlockTest 30: [ RUN ] IndexBlockTest.CreatesUnknownBlock 30: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms) 30: [ RUN ] IndexBlockTest.CreatesAtomBlock 30: [ OK ] IndexBlockTest.CreatesAtomBlock (1 ms) 30: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology 30: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms) 30: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology 30: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (0 ms) 30: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology 30: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms) 30: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology 30: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms) 30: [ RUN ] IndexBlockTest.CreatesSingleBlock 30: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) 30: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 30: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) 30: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 30: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) 30: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 30: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 30: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 30: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) 30: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 30: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 30: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 30: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 30: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 30: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 30: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 30: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 30: [----------] 15 tests from IndexBlockTest (3 ms total) 30: 30: [----------] 11 tests from IndexMapTest 30: [ RUN ] IndexMapTest.InitializesAtomBlock 30: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms) 30: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 30: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms) 30: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 30: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (1 ms) 30: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 30: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) 30: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 30: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms) 30: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 30: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms) 30: [ RUN ] IndexMapTest.InitializesMoleculeBlock 30: [ OK ] IndexMapTest.InitializesMoleculeBlock (1 ms) 30: [ RUN ] IndexMapTest.MapsSingleBlock 30: [ OK ] IndexMapTest.MapsSingleBlock (0 ms) 30: [ RUN ] IndexMapTest.MapsResidueBlocks 30: [ OK ] IndexMapTest.MapsResidueBlocks (0 ms) 30: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 30: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (1 ms) 30: [ RUN ] IndexMapTest.HandlesMultipleRequests 30: [ OK ] IndexMapTest.HandlesMultipleRequests (1 ms) 30: [----------] 11 tests from IndexMapTest (4 ms total) 30: 30: [----------] 3 tests from IndexGroupsAndNamesTest 30: [ RUN ] IndexGroupsAndNamesTest.containsNames 30: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms) 30: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing 30: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms) 30: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect 30: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms) 30: [----------] 3 tests from IndexGroupsAndNamesTest (0 ms total) 30: 30: [----------] 15 tests from NeighborhoodSearchTest 30: [ RUN ] NeighborhoodSearchTest.SimpleSearch 30: [ OK ] NeighborhoodSearchTest.SimpleSearch (21 ms) 30: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 30: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (42 ms) 30: [ RUN ] NeighborhoodSearchTest.GridSearchBox 30: [ OK ] NeighborhoodSearchTest.GridSearchBox (4 ms) 30: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 30: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (13 ms) 30: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 30: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (6 ms) 30: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 30: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (2 ms) 30: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 30: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (4 ms) 30: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 30: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 30: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 30: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (82 ms) 30: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 30: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) 30: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 30: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 30: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 30: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 30: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 30: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 30: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 30: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (4 ms) 30: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 30: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (1 ms) 30: [----------] 15 tests from NeighborhoodSearchTest (179 ms total) 30: 30: [----------] 12 tests from PositionCalculationTest 30: [ RUN ] PositionCalculationTest.ComputesAtomPositions 30: [ OK ] PositionCalculationTest.ComputesAtomPositions (1 ms) 30: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 30: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms) 30: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 30: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (1 ms) 30: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 30: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms) 30: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 30: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms) 30: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 30: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms) 30: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 30: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms) 30: [ RUN ] PositionCalculationTest.ComputesPositionMask 30: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms) 30: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 30: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (1 ms) 30: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 30: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms) 30: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 30: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (0 ms) 30: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 30: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (1 ms) 30: [----------] 12 tests from PositionCalculationTest (5 ms total) 30: 30: [----------] 29 tests from SelectionCollectionTest 30: [ RUN ] SelectionCollectionTest.HandlesNoSelections 30: [ OK ] SelectionCollectionTest.HandlesNoSelections (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 30: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (3 ms) 30: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 30: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 30: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (1 ms) 30: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 30: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 30: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 30: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (1 ms) 30: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 30: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (1 ms) 30: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 30: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 30: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 30: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (1 ms) 30: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 30: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (1 ms) 30: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 30: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 30: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 30: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 30: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (1 ms) 30: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 30: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 30: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (1 ms) 30: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 30: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (0 ms) 30: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 30: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (0 ms) 30: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 30: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (0 ms) 30: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 30: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (0 ms) 30: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 30: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (1 ms) 30: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 30: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (0 ms) 30: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 30: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 30: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 30: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 30: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (1 ms) 30: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 30: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (0 ms) 30: [----------] 29 tests from SelectionCollectionTest (15 ms total) 30: 30: [----------] 14 tests from SelectionCollectionInteractiveTest 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 30: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (1 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 30: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (0 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 30: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (1 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 30: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (0 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 30: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (1 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 30: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (1 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 30: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (1 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 30: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (1 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 30: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (0 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 30: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (1 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 30: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (1 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 30: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (0 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 30: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (1 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 30: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (0 ms) 30: [----------] 14 tests from SelectionCollectionInteractiveTest (9 ms total) 30: 30: [----------] 66 tests from SelectionCollectionDataTest 30: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 30: [ OK ] SelectionCollectionDataTest.HandlesAllNone (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 30: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesResnr 30: [ OK ] SelectionCollectionDataTest.HandlesResnr (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 30: [ OK ] SelectionCollectionDataTest.HandlesResIndex (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 30: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 30: [ OK ] SelectionCollectionDataTest.HandlesAtomname (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 30: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 30: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesChain 30: [ OK ] SelectionCollectionDataTest.HandlesChain (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesMass 30: [ OK ] SelectionCollectionDataTest.HandlesMass (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesCharge 30: [ OK ] SelectionCollectionDataTest.HandlesCharge (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 30: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 30: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 30: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesBeta 30: [ OK ] SelectionCollectionDataTest.HandlesBeta (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesResname 30: [ OK ] SelectionCollectionDataTest.HandlesResname (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 30: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (2 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 30: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 30: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 30: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (2 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 30: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 30: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 30: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 30: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (7 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 30: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (29 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 30: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (3 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 30: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (3 ms) 30: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 30: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (2 ms) 30: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 30: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 30: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 30: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 30: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 30: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (2 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 30: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (2 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 30: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (2 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 30: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 30: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 30: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 30: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 30: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 30: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 30: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 30: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 30: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (2 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 30: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 30: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 30: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 30: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 30: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 30: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 30: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 30: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (2 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 30: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (2 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 30: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 30: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (2 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 30: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (2 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 30: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 30: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (2 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 30: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (2 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 30: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 30: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 30: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 30: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 30: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 30: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 30: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (1 ms) 30: [----------] 66 tests from SelectionCollectionDataTest (120 ms total) 30: 30: [----------] 17 tests from SelectionOptionTest 30: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 30: [ OK ] SelectionOptionTest.ParsesSimpleSelection (1 ms) 30: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 30: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 30: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (1 ms) 30: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 30: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (0 ms) 30: [ RUN ] SelectionOptionTest.ChecksEmptySelections 30: [ OK ] SelectionOptionTest.ChecksEmptySelections (1 ms) 30: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 30: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesTooManySelections 30: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 30: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 30: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesAdjuster 30: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 30: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (1 ms) 30: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 30: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 30: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 30: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 30: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 30: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 30: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (1 ms) 30: [----------] 17 tests from SelectionOptionTest (7 ms total) 30: 30: [----------] 9 tests from SelectionFileOptionTest 30: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 30: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (0 ms) 30: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 30: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (1 ms) 30: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 30: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) 30: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 30: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (0 ms) 30: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 30: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (1 ms) 30: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 30: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (0 ms) 30: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 30: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (1 ms) 30: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 30: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (25 ms) 30: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 30: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (0 ms) 30: [----------] 9 tests from SelectionFileOptionTest (28 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 192 tests from 11 test cases ran. (370 ms total) 30: [ PASSED ] 192 tests. 30/30 Test #30: SelectionUnitTests ............... Passed 0.43 sec 100% tests passed, 0 tests failed out of 30 Label Time Summary: GTest = 3.32 sec*proc (30 tests) MpiTest = 0.43 sec*proc (3 tests) UnitTest = 3.32 sec*proc (30 tests) Total Test time (real) = 3.55 sec touch build-mpich dh_testdir /usr/bin/make -j4 -C build/openmpi make[1]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/cmake -S/build/gromacs-5atmZb/gromacs-2020.6 -B/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/CMakeFiles /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/CMakeFiles/release-version-info.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/selection /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color= Scanning dependencies of target release-version-info make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.6-Debian-2020.6-2 -D PROJECT_SOURCE_DIR=/build/gromacs-5atmZb/gromacs-2020.6 -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2020.6-2 -P /build/gromacs-5atmZb/gromacs-2020.6/cmake/gmxGenerateVersionInfoRelease.cmake Scanning dependencies of target lmfit_objlib make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++14 -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit/lmmin.cpp Scanning dependencies of target scanner make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build Scanning dependencies of target thread_mpi make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/selection && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/parser.cpp make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/errhandler.cpp [ 0%] Built target release-version-info cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/tmpi_malloc.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/atomic.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/selection && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/scanner.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/lock.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/pthreads.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/system_error.cpp make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 1%] Built target thread_mpi /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= Scanning dependencies of target tng_io_obj make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/bwlzh.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/bwt.c make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 1%] Built target lmfit_objlib /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/linearalgebra /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= Scanning dependencies of target linearalgebra make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/linearalgebra && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra/eigensolver.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/coder.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/dict.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/fixpoint.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/linearalgebra && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/linearalgebra && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra/matrix.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/huffman.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/huffmem.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/linearalgebra && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra/nrjac.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/lz77.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/merge_sort.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/mtf.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/rle.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/tng_compress.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/vals16.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/warnmalloc.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/linearalgebra && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/widemuldiv.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/xtc2.c make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 1%] Built target scanner /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color= Scanning dependencies of target modularsimulator make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/checkpointhelper.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/xtc3.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/compositesimulatorelement.cpp make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 1%] Built target linearalgebra /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun_objlib make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/programs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/mdrun.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/computeglobalselement.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/programs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/nonbonded_bench.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/lib/tng_io.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/lib/md5.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/constraintelement.cpp make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 2%] Built target mdrun_objlib cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/domdechelper.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/energyelement.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/energyelement.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/forceelement.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/freeenergyperturbationelement.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security 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/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/propagator.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/shellfcelement.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/shellfcelement.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/signallers.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem 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CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/topologyholder.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/trajectoryelement.cpp make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 5%] Built target tng_io_obj cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/vrescalethermostat.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/vrescalethermostat.cpp make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 8%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/VersionInfo.cmake -D VERSION_CMAKEIN=/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/gromacs-5atmZb/gromacs-2020.6/cmake/gmxConfigureVersionInfo.cmake cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= 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/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/benchmark/bench_system.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/grid.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/gridset.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernel_common.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kerneldispatch.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_reference/kernel_ref.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops 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-fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_prune.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops 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-fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_prune.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem 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/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/lincs.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/md_support.cpp /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/forcerec.cpp: In function ‘void __static_initialization_and_destruction_0(int, int)’: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/forcerec.cpp:103:16: warning: ignoring return value of ‘char* getenv(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 103 | (getenv("GMX_GPU_PME_PP_COMMS") != nullptr) && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/mdatoms.cpp 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/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/ewald_utils.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -c 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/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/pme_gather.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/pme_grid.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/pme_load_balancing.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/pme_only.cpp /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/pme_only.cpp: In function ‘void __static_initialization_and_destruction_0(int, int)’: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/pme_only.cpp:104:16: warning: ignoring return value of ‘char* getenv(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 104 | (getenv("GMX_GPU_PME_PP_COMMS") != nullptr) && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include 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/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/pme_redistribute.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/pme_solve.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/pme_spline_work.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/pme_spread.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/pme_gpu_program.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/pme_force_sender_gpu_impl.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/pme_gpu_program_impl.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem 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/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fft/fft.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem 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'/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/selection /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color= Scanning dependencies of target release-version-info make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' cd /build/gromacs-5atmZb/gromacs-2020.6 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.6-Debian-2020.6-2 -D PROJECT_SOURCE_DIR=/build/gromacs-5atmZb/gromacs-2020.6 -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2020.6-2 -P /build/gromacs-5atmZb/gromacs-2020.6/cmake/gmxGenerateVersionInfoRelease.cmake Scanning dependencies of target scanner make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/selection && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/parser.cpp make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' Scanning dependencies of target thread_mpi make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/errhandler.cpp Scanning dependencies of target lmfit_objlib make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build [ 0%] Built target release-version-info /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++14 -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit/lmmin.cpp make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= Scanning dependencies of target tng_io_obj make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/bwlzh.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/tmpi_malloc.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/atomic.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/lock.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/pthreads.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/src/system_error.cpp make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' [ 1%] Built target thread_mpi /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/linearalgebra /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= Scanning dependencies of target linearalgebra make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra/eigensolver.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/bwt.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/coder.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra/gmx_arpack.cpp make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' [ 1%] Built target lmfit_objlib cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/dict.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/fixpoint.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/huffman.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops 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-DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra/nrjac.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/lz77.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/merge_sort.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/mtf.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/rle.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/tng_compress.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/vals16.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/warnmalloc.c /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color= Scanning dependencies of target modularsimulator make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/checkpointhelper.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/compositesimulatorelement.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/selection && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/scanner.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/computeglobalselement.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/widemuldiv.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/xtc2.c make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' [ 1%] Built target linearalgebra /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun_objlib make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/programs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/mdrun.cpp make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' [ 1%] Built target scanner cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/programs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/programs/mdrun/nonbonded_bench.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/compression/xtc3.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/constraintelement.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/lib/tng_io.c make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' [ 2%] Built target mdrun_objlib cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/src/lib/md5.c cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/domdechelper.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/energyelement.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/energyelement.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/forceelement.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/freeenergyperturbationelement.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/modularsimulator.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/propagator.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/shellfcelement.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/shellfcelement.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/signallers.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/statepropagatordata.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/topologyholder.cpp make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' [ 5%] Built target tng_io_obj cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/trajectoryelement.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/vrescalethermostat.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator/vrescalethermostat.cpp make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' [ 8%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/gromacs-5atmZb/gromacs-2020.6/cmake/gmxConfigureVersionInfo.cmake cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= Scanning dependencies of target libgromacs make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/alignedallocator.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem 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-isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_reference/kernel_ref.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem 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-I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem 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/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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-I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 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/usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd 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/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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-funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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-I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd 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/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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-I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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-I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp cd 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/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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-std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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-I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd 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/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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-I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. 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/build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem 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/build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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/build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem 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-I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o 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/build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/lincs.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem 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GMX_GPU_CUDA); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c 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/build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/pme_only.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/tng/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/lmfit -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/pme_pp.cpp /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/pme_only.cpp: In function ‘void __static_initialization_and_destruction_0(int, int)’: /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/pme_only.cpp:104:16: warning: ignoring return value of ‘char* getenv(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 104 | (getenv("GMX_GPU_PME_PP_COMMS") != nullptr) && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/tng_io/include 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directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 0%] Built target scanner [ 0%] Built target lmfit_objlib /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend [ 1%] Built target thread_mpi make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 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'/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 3%] Built target modularsimulator make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' make[4]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[4]: Entering directory 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'/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= Scanning dependencies of target gtest make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build.make src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/external/googletest/googlemock/gtest && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wshadow -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=c++14 -o CMakeFiles/gtest.dir/src/gtest-all.cc.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/src/gtest-all.cc make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 72%] Built target libgromacs cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/external/googletest/googlemock/gtest && /usr/bin/cmake -P CMakeFiles/gtest.dir/cmake_clean_target.cmake cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/external/googletest/googlemock/gtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../../lib/libgtest.a CMakeFiles/gtest.dir/src/gtest-all.cc.o /usr/bin/ranlib ../../../../../lib/libgtest.a make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 72%] Built target gtest /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/external/googletest/googlemock /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/external/googletest/googlemock/CMakeFiles/gmock.dir/DependInfo.cmake --color= Scanning dependencies of target gmock make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/external/googletest/googlemock && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_CAN_STREAM_RESULTS=0 -D_GNU_SOURCE=1 -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock -I/build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wshadow -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated-copy -std=c++14 -o CMakeFiles/gmock.dir/src/gmock-all.cc.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/src/gmock-all.cc cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/external/googletest/googlemock && /usr/bin/cmake -P CMakeFiles/gmock.dir/cmake_clean_target.cmake cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libgmock.a CMakeFiles/gmock.dir/src/gmock-all.cc.o /usr/bin/ranlib ../../../../lib/libgmock.a make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 73%] Built target gmock /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/testutils /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/testutils /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/testutils/CMakeFiles/testutils.dir/DependInfo.cmake --color= Scanning dependencies of target testutils make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/cmdlinetest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/cmdlinetest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/conftest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/conftest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem 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CMakeFiles/testutils.dir/refdata.cpp.o CMakeFiles/testutils.dir/refdata_xml.cpp.o CMakeFiles/testutils.dir/simulationdatabase.cpp.o CMakeFiles/testutils.dir/stdiohelper.cpp.o CMakeFiles/testutils.dir/stringtest.cpp.o CMakeFiles/testutils.dir/testasserts.cpp.o CMakeFiles/testutils.dir/testfilemanager.cpp.o CMakeFiles/testutils.dir/testfileredirector.cpp.o CMakeFiles/testutils.dir/testinit.cpp.o CMakeFiles/testutils.dir/testmatchers.cpp.o CMakeFiles/testutils.dir/testoptions.cpp.o CMakeFiles/testutils.dir/textblockmatchers.cpp.o CMakeFiles/testutils.dir/tprfilegenerator.cpp.o CMakeFiles/testutils.dir/xvgtest.cpp.o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o /usr/bin/ranlib ../../lib/libtestutils.a make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 76%] Built target testutils /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/depend /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/depend /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/testutils/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/selection/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target testutils-mpi-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/testutils/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/testutils/tests/CMakeFiles/testutils-test.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/tests/mpitest.cpp Scanning dependencies of target utility-mpi-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/physicalnodecommunicator_mpi.cpp Scanning dependencies of target selection-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build Scanning dependencies of target testutils-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/selection/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/tests/indexutil.cpp /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/interactivetest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/tests/interactivetest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../lib/libgtest.a cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/tests/refdata_tests.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 76%] Built target utility-mpi-test /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 77%] Built target testutils-mpi-test /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/DependInfo.cmake --color= Scanning dependencies of target utility-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/alignedallocator.cpp Scanning dependencies of target mdlib-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/calc_verletbuf.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/selection/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/tests/nbsearch.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/constr.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/tests/testasserts_tests.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/arrayref.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/selection/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/tests/poscalc.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/constrtestdata.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/tests/xvgtest_tests.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/../external/tinyxml2 -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/constrtestrunners.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/selection/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/tests/selectioncollection.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-test.dir/interactivetest.cpp.o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../lib/libgtest.a make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 77%] Built target testutils-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/selection/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/tests/selectionoption.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/ebin.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/energyoutput.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/expanded.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/selection/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection/tests/toputils.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/bitmask32.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/selection/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/selection-test.dir/indexutil.cpp.o CMakeFiles/selection-test.dir/nbsearch.cpp.o CMakeFiles/selection-test.dir/poscalc.cpp.o CMakeFiles/selection-test.dir/selectioncollection.cpp.o CMakeFiles/selection-test.dir/selectionoption.cpp.o CMakeFiles/selection-test.dir/toputils.cpp.o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/leapfrog.cpp /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/applied_forces/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/applied_forces/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake --color= Scanning dependencies of target applied_forces-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/applied_forces/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfitting.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/applied_forces/tests/densityfitting.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 78%] Built target selection-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/leapfrogtestdata.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/applied_forces/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfittingoptions.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/applied_forces/tests/densityfittingoptions.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/applied_forces/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/applied_forces/tests/densityfittingamplitudelookup.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/settle.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/applied_forces/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/applied_forces/tests/electricfield.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/settletestdata.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/applied_forces/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/bitmask64.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/applied_forces-test.dir/densityfitting.cpp.o CMakeFiles/applied_forces-test.dir/densityfittingoptions.cpp.o CMakeFiles/applied_forces-test.dir/densityfittingamplitudelookup.cpp.o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/settletestrunners.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 78%] Built target applied_forces-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/shake.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/bitmask128.cpp /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/onlinehelp/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/onlinehelp/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color= Scanning dependencies of target onlinehelp-test-shared make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/onlinehelp/tests/mock_helptopic.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/cstringutil.cpp /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/domdec/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/domdec/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color= Scanning dependencies of target domdec-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/domdec/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/domdec/tests/hashedmap.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/simulationsignal.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o /usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 78%] Built target onlinehelp-test-shared cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/updategroups.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/defaultinitializationallocator.cpp /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/ewald/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color= Scanning dependencies of target ewald-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/domdec/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/domdec/tests/localatomsetmanager.cpp make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/tests/pmebsplinetest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/enumerationhelpers.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdlib/tests/updategroupscog.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/domdec/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/domdec-test.dir/hashedmap.cpp.o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/fixedcapacityvector.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 78%] Built target domdec-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/inmemoryserializer.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/tests/pmegathertest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/constr.cpp.o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o CMakeFiles/mdlib-test.dir/ebin.cpp.o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o CMakeFiles/mdlib-test.dir/expanded.cpp.o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o CMakeFiles/mdlib-test.dir/settle.cpp.o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o CMakeFiles/mdlib-test.dir/shake.cpp.o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o CMakeFiles/mdlib-test.dir/updategroups.cpp.o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/tests/pmesolvetest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/keyvaluetreeserializer.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 80%] Built target mdlib-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/keyvaluetreetransform.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/logger.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/logger.cpp /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fft/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/fft/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color= Scanning dependencies of target fft-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/fft/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/fft/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fft-test.dir/fft.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fft/tests/fft.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/tests/pmesplinespreadtest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/tests/pmetestcommon.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/mutex.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/fft/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/fft/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/path.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/path.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/fft-test.dir/fft.cpp.o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 80%] Built target fft-test /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gpu_utils/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/gpu_utils/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color= Scanning dependencies of target gpu_utils-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/gputest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gpu_utils/tests/gputest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gpu_utils/tests/clfftinitializer.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/physicalnodecommunicator.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/stringutil.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gpu_utils/tests/hostallocator.cpp /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/hardware/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/hardware/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color= Scanning dependencies of target hardware-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/hardware/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/hardware/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/hardware/tests/hardwaretopology.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/ewald/tests/testhardwarecontexts.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/hardware/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/hardware/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 81%] Built target ewald-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/textreader.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 81%] Built target hardware-test /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/math/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color= Scanning dependencies of target math-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/arrayrefwithpadding.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/textwriter.cpp /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdrunutility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-test-shared make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/coordinatetransformation.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/utility/tests/typetraits.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-test.dir/alignedallocator.cpp.o CMakeFiles/utility-test.dir/arrayref.cpp.o CMakeFiles/utility-test.dir/bitmask32.cpp.o CMakeFiles/utility-test.dir/bitmask64.cpp.o CMakeFiles/utility-test.dir/bitmask128.cpp.o CMakeFiles/utility-test.dir/cstringutil.cpp.o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/stringutil.cpp.o CMakeFiles/utility-test.dir/textreader.cpp.o CMakeFiles/utility-test.dir/textwriter.cpp.o CMakeFiles/utility-test.dir/typetraits.cpp.o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o /usr/bin/ranlib ../../../../lib/libmdrunutility-test-shared.a make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 82%] Built target mdrunutility-test-shared cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/densityfit.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/densityfit.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 85%] Built target utility-test /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdspan/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdspan/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdspan-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdspan/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdspan/tests/accessor_policy.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/gpu_utils/tests/devicetransfers.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdspan/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/extents.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdspan/tests/extents.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdspan/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/extensions.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdspan/tests/extensions.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/gpu_utils-test.dir/gputest.cpp.o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 85%] Built target gpu_utils-test /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/onlinehelp/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/onlinehelp/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/options/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/options/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color= Scanning dependencies of target onlinehelp-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/onlinehelp/tests/helpformat.cpp Scanning dependencies of target options-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/options/tests/abstractoptionstorage.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/dofit.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/dofit.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdspan/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/layouts.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdspan/tests/layouts.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/onlinehelp/tests/helpmanager.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/exponentialmovingaverage.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdspan/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/mdspan.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdspan/tests/mdspan.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/onlinehelp/tests/helpwritercontext.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/functions.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/functions.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgmock.a ../../../../lib/libgtest.a make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 86%] Built target onlinehelp-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/gausstransform.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/gausstransform.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/densityfittingforce.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/options/tests/filenameoption.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/invertmatrix.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/matrix.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/matrix.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/options/tests/filenameoptionmanager.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/option.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/options/tests/option.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdspan/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdspan/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/options/tests/optionsassigner.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o CMakeFiles/mdspan-test.dir/extents.cpp.o CMakeFiles/mdspan-test.dir/extensions.cpp.o CMakeFiles/mdspan-test.dir/layouts.cpp.o CMakeFiles/mdspan-test.dir/mdspan.cpp.o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 86%] Built target mdspan-test /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/pbcutil/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/pbcutil/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake --color= Scanning dependencies of target pbcutil-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/pbcutil/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/pbcutil/tests/pbc.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/multidimarray.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/pbcutil/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/pbcutil/tests/pbcenums.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/pbcutil/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/options/tests/repeatingsection.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/pbcutil-test.dir/pbc.cpp.o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 86%] Built target pbcutil-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/paddedvector.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/math/tests/vectypes.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/random/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/random/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color= Scanning dependencies of target random-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/random/tests/exponentialdistribution.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/options/tests/timeunitmanager.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/options/tests/treesupport.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/random/tests/gammadistribution.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/random/tests/normaldistribution.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/seed.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/random/tests/seed.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o CMakeFiles/options-test.dir/filenameoption.cpp.o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o CMakeFiles/options-test.dir/option.cpp.o CMakeFiles/options-test.dir/optionsassigner.cpp.o CMakeFiles/options-test.dir/repeatingsection.cpp.o CMakeFiles/options-test.dir/timeunitmanager.cpp.o CMakeFiles/options-test.dir/treesupport.cpp.o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 87%] Built target options-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/random/tests/tabulatednormaldistribution.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/threefry.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/random/tests/threefry.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/random/tests/uniformintdistribution.cpp /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/restraint/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/restraint/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color= Scanning dependencies of target restraintpotential-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/restraint/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/restraint/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/restraint/tests/manager.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/random/tests/uniformrealdistribution.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/restraint/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/restraint/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o CMakeFiles/math-test.dir/densityfit.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/gausstransform.cpp.o CMakeFiles/math-test.dir/densityfittingforce.cpp.o CMakeFiles/math-test.dir/invertmatrix.cpp.o CMakeFiles/math-test.dir/matrix.cpp.o CMakeFiles/math-test.dir/multidimarray.cpp.o CMakeFiles/math-test.dir/paddedvector.cpp.o CMakeFiles/math-test.dir/vectypes.cpp.o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/restraintpotential-test.dir/manager.cpp.o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 87%] Built target restraintpotential-test /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/tables/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/tables/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 89%] Built target math-test /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/taskassignment/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/taskassignment/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color= Scanning dependencies of target taskassignment-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/taskassignment/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/taskassignment/tests/usergpuids.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/taskassignment/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp Scanning dependencies of target table-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/tables/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/tables/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/tables/tests/splinetable.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/random-test.dir/exponentialdistribution.cpp.o CMakeFiles/random-test.dir/gammadistribution.cpp.o CMakeFiles/random-test.dir/normaldistribution.cpp.o CMakeFiles/random-test.dir/seed.cpp.o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o CMakeFiles/random-test.dir/threefry.cpp.o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/tables/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/tables/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 90%] Built target random-test /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/topology/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/topology/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake --color= Scanning dependencies of target topology-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/topology/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/topology/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/topology/tests/exclusionblocks.cpp /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/pulling/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/pulling/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color= Scanning dependencies of target pull-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/pulling/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/pulling/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pull-test.dir/pull.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/pulling/tests/pull.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/topology/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/topology/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/topology/tests/mtop.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/pulling/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/pulling/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/pull-test.dir/pull.cpp.o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/topology/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/topology/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/topology/tests/symtab.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 91%] Built target pull-test /usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/awh/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/awh/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color= Scanning dependencies of target awh-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/awh/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/bias.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/awh/tests/bias.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 92%] Built target taskassignment-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/awh/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/awh/tests/biasstate.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/topology/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/topology/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/topology-test.dir/exclusionblocks.cpp.o CMakeFiles/topology-test.dir/mtop.cpp.o CMakeFiles/topology-test.dir/symtab.cpp.o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/awh/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/grid.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/awh/tests/grid.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 93%] Built target topology-test /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color= Scanning dependencies of target simd-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/bootstrap_loadstore.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/awh/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/compat/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/compat/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color= Scanning dependencies of target compat-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/compat/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-unused-member-function -o CMakeFiles/compat-test.dir/optional.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/compat/tests/optional.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/table-test.dir/splinetable.cpp.o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/grid.cpp.o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/awh-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/base.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/base.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 93%] Built target table-test /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color= Scanning dependencies of target fileio-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio/tests/confio.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 94%] Built target awh-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/compat/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/compat/tests/pointers.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd_floatingpoint.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio/tests/filemd5.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd_floatingpoint_util.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio/tests/mrcserializer.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/compat/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/string_view.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/compat/tests/string_view.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio/tests/mrcdensitymap.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio/tests/mrcdensitymapheader.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd_vector_operations.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/compat/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd_math.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd_memory.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio/tests/readinp.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio/tests/fileioxdrserializer.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1 cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio/tests/tngio.cpp /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/compat-test.dir/optional.cpp.o CMakeFiles/compat-test.dir/pointers.cpp.o CMakeFiles/compat-test.dir/string_view.cpp.o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 95%] Built target compat-test /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color= Scanning dependencies of target commandline-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd_integer.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 96%] Built target fileio-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdrunutility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-mpi-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd4.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd4_floatingpoint.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd4_vector_operations.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgmock.a ../../../../lib/libgtest.a cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/simd4_math.cpp make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 96%] Built target mdrunutility-mpi-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdrunutility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-test make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/mdrunutility/tests/threadaffinity.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/scalar.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/scalar_util.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/simd/tests/scalar_math.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgmock.a ../../../../lib/libgtest.a make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 96%] Built target mdrunutility-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/tests/cmdlineparser.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/filenm.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/tests/filenm.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/commandline/tests/pargs.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/base.cpp.o CMakeFiles/simd-test.dir/simd.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4_math.cpp.o CMakeFiles/simd-test.dir/scalar.cpp.o CMakeFiles/simd-test.dir/scalar_util.cpp.o CMakeFiles/simd-test.dir/scalar_math.cpp.o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgtest.a make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 98%] Built target simd-test cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src -I/build/gromacs-5atmZb/gromacs-2020.6/src -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/thread_mpi/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googlemock/include -isystem /build/gromacs-5atmZb/gromacs-2020.6/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-5atmZb/gromacs-2020.6/src/testutils/unittest_main.cpp cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-5atmZb/gromacs-2020.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o CMakeFiles/commandline-test.dir/filenm.cpp.o CMakeFiles/commandline-test.dir/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so ../../../../lib/libgmock.a ../../../../lib/libgtest.a make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [100%] Built target commandline-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/CMakeFiles/tests.dir/DependInfo.cmake --color= Scanning dependencies of target tests make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [100%] Built target tests make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/cmake -E cmake_progress_start /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/CMakeFiles 0 make[2]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' make[1]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' (cd build/openmpi ; LD_LIBRARY_PATH=/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/lib \ OMPI_MCA_plm_rsh_agent=/bin/false \ OMPI_MCA_rmaps_base_oversubscribe=1 \ ctest -V || dpkg-architecture -i hurd-i386 || dpkg-architecture -i x32 ) UpdateCTestConfiguration from :/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/DartConfiguration.tcl Parse Config file:/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/DartConfiguration.tcl UpdateCTestConfiguration from :/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/DartConfiguration.tcl Parse Config file:/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/DartConfiguration.tcl Test project /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: TestUtilsUnitTests 1: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/bin/testutils-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/Testing/Temporary/TestUtilsUnitTests.xml" 1: Test timeout computed to be: 30 1: [==========] Running 59 tests from 5 test cases. 1: [----------] Global test environment set-up. 1: [----------] 10 tests from InteractiveTestHelperTest 1: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 1: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (51 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (5 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 1: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 1: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 1: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) 1: [----------] 10 tests from InteractiveTestHelperTest (59 ms total) 1: 1: [----------] 34 tests from ReferenceDataTest 1: [ RUN ] ReferenceDataTest.HandlesSimpleData 1: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 1: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 1: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesStringBlockData 1: [ OK ] ReferenceDataTest.HandlesStringBlockData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesVectorData 1: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceData 1: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 1: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesIncorrectData 1: [ OK ] ReferenceDataTest.HandlesIncorrectData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 1: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesMissingData 1: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedData 1: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesAnys 1: [ OK ] ReferenceDataTest.HandlesAnys (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 1: [ OK ] ReferenceDataTest.HandlesKeyValueTree (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue 1: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType 1: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 1: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 1: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 1: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 1: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 1: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 1: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 1: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 1: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 1: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesReadingValues 1: [ OK ] ReferenceDataTest.HandlesReadingValues (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (0 ms) 1: [----------] 34 tests from ReferenceDataTest (7 ms total) 1: 1: [----------] 7 tests from FloatingPointDifferenceTest 1: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 1: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 1: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 1: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 1: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 1: [ OK ] FloatingPointDifferenceTest.HandlesNaN (1 ms) 1: [----------] 7 tests from FloatingPointDifferenceTest (1 ms total) 1: 1: [----------] 4 tests from FloatingPointToleranceTest 1: [ RUN ] FloatingPointToleranceTest.UlpTolerance 1: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 1: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 1: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 1: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 1: 1: [----------] 4 tests from XvgTests 1: [ RUN ] XvgTests.CreateFile 1: [ OK ] XvgTests.CreateFile (0 ms) 1: [ RUN ] XvgTests.CheckMissing 1: [ OK ] XvgTests.CheckMissing (0 ms) 1: [ RUN ] XvgTests.CheckExtra 1: [ OK ] XvgTests.CheckExtra (0 ms) 1: [ RUN ] XvgTests.ReadIncorrect 1: [ OK ] XvgTests.ReadIncorrect (1 ms) 1: [----------] 4 tests from XvgTests (1 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 59 tests from 5 test cases ran. (68 ms total) 1: [ PASSED ] 59 tests. 1/30 Test #1: TestUtilsUnitTests ............... Passed 2.44 sec test 2 Start 2: TestUtilsMpiUnitTests 2: Test command: /usr/bin/mpiexec.openmpi "-np" "2" "-host" "localhost" "/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/bin/testutils-mpi-test" "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/Testing/Temporary/TestUtilsMpiUnitTests.xml" 2: Test timeout computed to be: 30 2: [==========] Running 1 test from 1 test case. 2: [----------] Global test environment set-up. 2: [----------] 1 test from MpiSelfTest 2: [ RUN ] MpiSelfTest.Runs 2: [ OK ] MpiSelfTest.Runs (0 ms) 2: [----------] 1 test from MpiSelfTest (0 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 1 test from 1 test case ran. (0 ms total) 2: [ PASSED ] 1 test. 2/30 Test #2: TestUtilsMpiUnitTests ............ Passed 0.60 sec test 3 Start 3: UtilityUnitTests 3: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/bin/utility-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/Testing/Temporary/UtilityUnitTests.xml" 3: Test timeout computed to be: 30 3: [==========] Running 347 tests from 56 test cases. 3: [----------] Global test environment set-up. 3: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 3: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/0.Move 3: [ OK ] AllocatorTest/0.Move (0 ms) 3: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/0 (1 ms total) 3: 3: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 3: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/1.Move 3: [ OK ] AllocatorTest/1.Move (0 ms) 3: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/1 (0 ms total) 3: 3: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 3: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/2.Move 3: [ OK ] AllocatorTest/2.Move (0 ms) 3: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/2 (0 ms total) 3: 3: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 3: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/3.Move 3: [ OK ] AllocatorTest/3.Move (0 ms) 3: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/3 (0 ms total) 3: 3: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 3: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/4.Move 3: [ OK ] AllocatorTest/4.Move (0 ms) 3: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/4 (0 ms total) 3: 3: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 3: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 3: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 3: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 3: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 3: [ RUN ] AllocatorTest/5.Move 3: [ OK ] AllocatorTest/5.Move (0 ms) 3: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 3: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 3: [----------] 5 tests from AllocatorTest/5 (0 ms total) 3: 3: [----------] 1 test from AllocatorUntypedTest 3: [ RUN ] AllocatorUntypedTest.Comparison 3: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 3: [----------] 1 test from AllocatorUntypedTest (0 ms total) 3: 3: [----------] 1 test from EmptyArrayRefTest 3: [ RUN ] EmptyArrayRefTest.IsEmpty 3: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 3: [----------] 1 test from EmptyArrayRefTest (0 ms total) 3: 3: [----------] 1 test from EmptyConstArrayRefTest 3: [ RUN ] EmptyConstArrayRefTest.IsEmpty 3: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 3: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 3: 3: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 3: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 3: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 3: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 3: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 3: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 3: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 3: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 3: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 3: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 3: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 3: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 3: 3: [----------] 2 tests from CStringUtilityTest 3: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison 3: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) 3: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength 3: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (1 ms) 3: [----------] 2 tests from CStringUtilityTest (1 ms total) 3: 3: [----------] 2 tests from DefaultInitializationAllocator 3: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization 3: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) 3: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization 3: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) 3: [----------] 2 tests from DefaultInitializationAllocator (0 ms total) 3: 3: [----------] 4 tests from EnumerationHelpersTest 3: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks 3: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms) 3: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks 3: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) 3: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe 3: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) 3: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks 3: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) 3: [----------] 4 tests from EnumerationHelpersTest (0 ms total) 3: 3: [----------] 9 tests from FixedCapacityVectorTest 3: [ RUN ] FixedCapacityVectorTest.IsEmpty 3: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) 3: [ RUN ] FixedCapacityVectorTest.PushWorks 3: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.PopWorks 3: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.ClearWorks 3: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks 3: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.AtThrows 3: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms) 3: [ RUN ] FixedCapacityVectorTest.IteratorWorks 3: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks 3: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) 3: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks 3: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) 3: [----------] 9 tests from FixedCapacityVectorTest (0 ms total) 3: 3: [----------] 5 tests from InMemorySerializerTest 3: [ RUN ] InMemorySerializerTest.Roundtrip 3: [ OK ] InMemorySerializerTest.Roundtrip (0 ms) 3: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap 3: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) 3: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap 3: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) 3: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap 3: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms) 3: [ RUN ] InMemorySerializerTest.SizeIsCorrect 3: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) 3: [----------] 5 tests from InMemorySerializerTest (0 ms total) 3: 3: [----------] 4 tests from KeyValueTreeSerializerTest 3: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 3: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms) 3: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 3: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) 3: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 3: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms) 3: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 3: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) 3: [----------] 4 tests from KeyValueTreeSerializerTest (0 ms total) 3: 3: [----------] 6 tests from TreeValueTransformTest 3: [ RUN ] TreeValueTransformTest.SimpleTransforms 3: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) 3: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 3: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (1 ms) 3: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 3: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms) 3: [ RUN ] TreeValueTransformTest.ObjectFromString 3: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) 3: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 3: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) 3: [ RUN ] TreeValueTransformTest.ScopedTransformRules 3: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 3: [----------] 6 tests from TreeValueTransformTest (1 ms total) 3: 3: [----------] 1 test from TreeValueTransformErrorTest 3: [ RUN ] TreeValueTransformErrorTest.ConversionError 3: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms) 3: [----------] 1 test from TreeValueTransformErrorTest (0 ms total) 3: 3: [----------] 7 tests from LoggerTest 3: [ RUN ] LoggerTest.EmptyLoggerWorks 3: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 3: [ RUN ] LoggerTest.LogsToStream 3: [ OK ] LoggerTest.LogsToStream (0 ms) 3: [ RUN ] LoggerTest.LogsToFile 3: [ OK ] LoggerTest.LogsToFile (18 ms) 3: [ RUN ] LoggerTest.LevelFilteringWorks 3: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 3: [ RUN ] LoggerTest.LogsToMultipleStreams 3: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 3: [ RUN ] LoggerTest.LogsToMultipleFiles 3: [ OK ] LoggerTest.LogsToMultipleFiles (1 ms) 3: [ RUN ] LoggerTest.LogsToStreamAndFile 3: [ OK ] LoggerTest.LogsToStreamAndFile (0 ms) 3: [----------] 7 tests from LoggerTest (19 ms total) 3: 3: [----------] 4 tests from MutexBasicTest 3: [ RUN ] MutexBasicTest.CanBeMade 3: [ OK ] MutexBasicTest.CanBeMade (0 ms) 3: [ RUN ] MutexBasicTest.CanBeLocked 3: [ OK ] MutexBasicTest.CanBeLocked (0 ms) 3: [ RUN ] MutexBasicTest.CanBeTryLocked 3: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms) 3: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard 3: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms) 3: [----------] 4 tests from MutexBasicTest (0 ms total) 3: 3: [----------] 3 tests from MutexTaskTest 3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock 3: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (0 ms) 3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread 3: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (0 ms) 3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread 3: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms) 3: [----------] 3 tests from MutexTaskTest (0 ms total) 3: 3: [----------] 2 tests from PathTest 3: [ RUN ] PathTest.StripSourcePrefixWorks 3: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 3: [ RUN ] PathTest.SearchOperationsWork 3: [ OK ] PathTest.SearchOperationsWork (0 ms) 3: [----------] 2 tests from PathTest (0 ms total) 3: 3: [----------] 2 tests from PhysicalNodeCommunicatorTest 3: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 3: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 3: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 3: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 3: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 3: 3: [----------] 9 tests from StringUtilityTest 3: [ RUN ] StringUtilityTest.StartsWith 3: [ OK ] StringUtilityTest.StartsWith (0 ms) 3: [ RUN ] StringUtilityTest.EndsWith 3: [ OK ] StringUtilityTest.EndsWith (0 ms) 3: [ RUN ] StringUtilityTest.StripSuffixIfPresent 3: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 3: [ RUN ] StringUtilityTest.StripString 3: [ OK ] StringUtilityTest.StripString (0 ms) 3: [ RUN ] StringUtilityTest.SplitString 3: [ OK ] StringUtilityTest.SplitString (0 ms) 3: [ RUN ] StringUtilityTest.SplitDelimitedString 3: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 3: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 3: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) 3: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive 3: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) 3: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength 3: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) 3: [----------] 9 tests from StringUtilityTest (0 ms total) 3: 3: [----------] 2 tests from FormatStringTest 3: [ RUN ] FormatStringTest.HandlesBasicFormatting 3: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 3: [ RUN ] FormatStringTest.HandlesLongStrings 3: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 3: [----------] 2 tests from FormatStringTest (0 ms total) 3: 3: [----------] 1 test from StringFormatterTest 3: [ RUN ] StringFormatterTest.HandlesBasicFormatting 3: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 3: [----------] 1 test from StringFormatterTest (0 ms total) 3: 3: [----------] 1 test from formatAndJoinTest 3: [ RUN ] formatAndJoinTest.Works 3: [ OK ] formatAndJoinTest.Works (0 ms) 3: [----------] 1 test from formatAndJoinTest (0 ms total) 3: 3: [----------] 1 test from JoinStringsTest 3: [ RUN ] JoinStringsTest.Works 3: [ OK ] JoinStringsTest.Works (0 ms) 3: [----------] 1 test from JoinStringsTest (0 ms total) 3: 3: [----------] 6 tests from ReplaceAllTest 3: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 3: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesNoMatches 3: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 3: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 3: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 3: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 3: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 3: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 3: [----------] 6 tests from ReplaceAllTest (0 ms total) 3: 3: [----------] 10 tests from TextLineWrapperTest 3: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 3: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 3: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 3: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 3: [ RUN ] TextLineWrapperTest.WrapsCorrectly 3: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms) 3: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 3: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (1 ms) 3: [ RUN ] TextLineWrapperTest.HandlesIndent 3: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 3: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 3: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) 3: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 3: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) 3: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 3: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) 3: [----------] 10 tests from TextLineWrapperTest (1 ms total) 3: 3: [----------] 6 tests from TextWriterTest 3: [ RUN ] TextWriterTest.WritesLines 3: [ OK ] TextWriterTest.WritesLines (0 ms) 3: [ RUN ] TextWriterTest.WritesLinesInParts 3: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 3: [ RUN ] TextWriterTest.WritesWrappedLines 3: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) 3: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 3: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 3: [ RUN ] TextWriterTest.TracksNewlines 3: [ OK ] TextWriterTest.TracksNewlines (0 ms) 3: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 3: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 3: [----------] 6 tests from TextWriterTest (0 ms total) 3: 3: [----------] 1 test from TypeTraitsTest 3: [ RUN ] TypeTraitsTest.IsIntegralConstant 3: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 3: [----------] 1 test from TypeTraitsTest (0 ms total) 3: 3: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 3: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 3: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 3: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 3: 3: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (1 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 3: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (1 ms total) 3: 3: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 3: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 3: 3: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms) 3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms) 3: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (0 ms total) 3: 3: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 3: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (0 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 347 tests from 56 test cases ran. (26 ms total) 3: [ PASSED ] 347 tests. 3/30 Test #3: UtilityUnitTests ................. Passed 0.54 sec test 4 Start 4: UtilityMpiUnitTests 4: Test command: /usr/bin/mpiexec.openmpi "-np" "4" "-host" "localhost" "/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/bin/utility-mpi-test" "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/Testing/Temporary/UtilityMpiUnitTests.xml" 4: Test timeout computed to be: 30 4: [==========] Running 2 tests from 1 test case. 4: [----------] Global test environment set-up. 4: [----------] 2 tests from PhysicalNodeCommunicatorTest 4: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 4: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 4: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 4: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 4: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 4: 4: [----------] Global test environment tear-down 4: [==========] 2 tests from 1 test case ran. (1 ms total) 4: [ PASSED ] 2 tests. 4/30 Test #4: UtilityMpiUnitTests .............. Passed 0.68 sec test 5 Start 5: MdlibUnitTest 5: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/bin/mdlib-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/Testing/Temporary/MdlibUnitTest.xml" 5: Test timeout computed to be: 30 5: [==========] Running 187 tests from 13 test cases. 5: [----------] Global test environment set-up. 5: [----------] 1 test from VerletBufferConstraintTest 5: [ RUN ] VerletBufferConstraintTest.EqualMasses 5: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 5: [----------] 1 test from VerletBufferConstraintTest (0 ms total) 5: 5: [----------] 2 tests from PrEbinTest 5: [ RUN ] PrEbinTest.HandlesAverages 5: [ OK ] PrEbinTest.HandlesAverages (32 ms) 5: [ RUN ] PrEbinTest.HandlesEmptyAverages 5: [ OK ] PrEbinTest.HandlesEmptyAverages (0 ms) 5: [----------] 2 tests from PrEbinTest (32 ms total) 5: 5: [----------] 4 tests from ShakeTest 5: [ RUN ] ShakeTest.ConstrainsOneBond 5: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) 5: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 5: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 5: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 5: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 5: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 5: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 5: [----------] 4 tests from ShakeTest (0 ms total) 5: 5: [----------] 1 test from NullSignalTest 5: [ RUN ] NullSignalTest.NullSignallerWorks 5: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 5: [----------] 1 test from NullSignalTest (0 ms total) 5: 5: [----------] 7 tests from SignalTest 5: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 5: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 5: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 5: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 5: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 5: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 5: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 5: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 5: [----------] 7 tests from SignalTest (0 ms total) 5: 5: [----------] 9 tests from UpdateGroups 5: [ RUN ] UpdateGroups.ethaneUA 5: [ OK ] UpdateGroups.ethaneUA (0 ms) 5: [ RUN ] UpdateGroups.methane 5: [ OK ] UpdateGroups.methane (0 ms) 5: [ RUN ] UpdateGroups.ethane 5: [ OK ] UpdateGroups.ethane (0 ms) 5: [ RUN ] UpdateGroups.butaneUA 5: [ OK ] UpdateGroups.butaneUA (0 ms) 5: [ RUN ] UpdateGroups.waterThreeSite 5: [ OK ] UpdateGroups.waterThreeSite (0 ms) 5: [ RUN ] UpdateGroups.waterFourSite 5: [ OK ] UpdateGroups.waterFourSite (0 ms) 5: [ RUN ] UpdateGroups.fourAtomsWithSettle 5: [ OK ] UpdateGroups.fourAtomsWithSettle (0 ms) 5: [ RUN ] UpdateGroups.waterFlexAngle 5: [ OK ] UpdateGroups.waterFlexAngle (0 ms) 5: [ RUN ] UpdateGroups.twoMoltypes 5: [ OK ] UpdateGroups.twoMoltypes (0 ms) 5: [----------] 9 tests from UpdateGroups (0 ms total) 5: 5: [----------] 1 test from UpdateGroupsCog 5: [ RUN ] UpdateGroupsCog.ComputesCogs 5: [ OK ] UpdateGroupsCog.ComputesCogs (1 ms) 5: [----------] 1 test from UpdateGroupsCog (1 ms total) 5: 5: [----------] 84 tests from WithParameters/ConstraintsTest 5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/0 5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/1 5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/2 5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/3 5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/2 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/3 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/3 (1 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/4 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/5 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/6 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/7 5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/2 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/3 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/4 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/5 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/6 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/7 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/8 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/8 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/9 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/9 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/10 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/10 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/11 5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/11 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/2 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/3 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/4 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/5 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/6 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/7 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/7 (1 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/8 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/8 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/9 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/9 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/10 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/10 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/11 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/11 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/12 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/12 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/13 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/13 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/14 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/14 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/15 5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/15 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/0 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/1 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/2 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/3 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/4 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/5 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/6 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/7 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/8 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/8 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/9 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/9 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/10 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/10 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/11 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/11 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/12 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/12 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/13 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/13 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/14 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/14 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/15 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/15 (1 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/16 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/16 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/17 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/17 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/18 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/18 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/19 5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/19 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/0 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/0 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/1 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/1 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/2 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/2 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/3 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/3 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/4 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/4 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/5 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/5 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/6 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/6 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/7 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/7 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/8 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/8 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/9 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/9 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/10 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/10 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/11 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/11 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/12 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/12 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/13 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/13 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/14 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/14 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/15 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/15 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/16 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/16 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/17 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/17 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/18 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/18 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/19 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/19 (1 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/20 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/20 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/21 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/21 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/22 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/22 (0 ms) 5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/23 5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/23 (0 ms) 5: [----------] 84 tests from WithParameters/ConstraintsTest (4 ms total) 5: 5: [----------] 11 tests from WithParameters/EnergyOutputTest 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (2 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (1 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (1 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3 5: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (0 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as single precision energy file 5: Reading energy frame 0 time 10.100 Reading energy frame 1 time 27.500 Reading energy frame 2 time 44.900 Reading energy frame 3 time 62.300 Reading energy frame 4 time 79.700 Reading energy frame 5 time 97.100 Reading energy frame 6 time 114.500 Reading energy frame 7 time 131.900 Reading energy frame 8 time 149.300 Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (9 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (3 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (3 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (3 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (2 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (4 ms) 5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10 5: Opened /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as single precision energy file 5: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (3 ms) 5: [----------] 11 tests from WithParameters/EnergyOutputTest (37 ms total) 5: 5: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms) 5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms) 5: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (0 ms total) 5: 5: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms) 5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms) 5: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (0 ms total) 5: 5: [----------] 16 tests from WithParameters/LeapFrogTest 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (1 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (2 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (4 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (0 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (1 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (1 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (1 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (1 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (1 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (1 ms) 5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (2 ms) 5: [----------] 16 tests from WithParameters/LeapFrogTest (18 ms total) 5: 5: [----------] 13 tests from WithParameters/SettleTest 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (1 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (1 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (1 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (1 ms) 5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (1 ms) 5: [----------] 13 tests from WithParameters/SettleTest (6 ms total) 5: 5: [----------] Global test environment tear-down 5: [==========] 187 tests from 13 test cases ran. (100 ms total) 5: [ PASSED ] 187 tests. 5/30 Test #5: MdlibUnitTest .................... Passed 0.67 sec test 6 Start 6: AppliedForcesUnitTest 6: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/bin/applied_forces-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/Testing/Temporary/AppliedForcesUnitTest.xml" 6: Test timeout computed to be: 30 6: [==========] Running 20 tests from 4 test cases. 6: [----------] Global test environment set-up. 6: [----------] 2 tests from DensityFittingTest 6: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows 6: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (0 ms) 6: [ RUN ] DensityFittingTest.SingleAtom 6: [ OK ] DensityFittingTest.SingleAtom (1 ms) 6: [----------] 2 tests from DensityFittingTest (1 ms total) 6: 6: [----------] 8 tests from DensityFittingOptionsTest 6: [ RUN ] DensityFittingOptionsTest.DefaultParameters 6: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) 6: [ RUN ] DensityFittingOptionsTest.OptionSetsActive 6: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms) 6: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive 6: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 6: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive 6: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (1 ms) 6: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup 6: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 6: [ RUN ] DensityFittingOptionsTest.InternalsToKvt 6: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) 6: [ RUN ] DensityFittingOptionsTest.KvtToInternal 6: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms) 6: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent 6: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms) 6: [----------] 8 tests from DensityFittingOptionsTest (1 ms total) 6: 6: [----------] 7 tests from DensityFittingAmplitudeLookupTest 6: [ RUN ] DensityFittingAmplitudeLookupTest.Unity 6: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.Charge 6: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.Masses 6: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign 6: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct 6: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign 6: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) 6: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct 6: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) 6: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total) 6: 6: [----------] 3 tests from ElectricFieldTest 6: [ RUN ] ElectricFieldTest.Static 6: [ OK ] ElectricFieldTest.Static (0 ms) 6: [ RUN ] ElectricFieldTest.Oscillating 6: [ OK ] ElectricFieldTest.Oscillating (1 ms) 6: [ RUN ] ElectricFieldTest.Pulsed 6: [ OK ] ElectricFieldTest.Pulsed (0 ms) 6: [----------] 3 tests from ElectricFieldTest (1 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 20 tests from 4 test cases ran. (3 ms total) 6: [ PASSED ] 20 tests. 6/30 Test #6: AppliedForcesUnitTest ............ Passed 0.55 sec test 7 Start 7: CommandLineUnitTests 7: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/bin/commandline-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/Testing/Temporary/CommandLineUnitTests.xml" 7: Test timeout computed to be: 30 7: [==========] Running 59 tests from 7 test cases. 7: [----------] Global test environment set-up. 7: [----------] 3 tests from CommandLineHelpModuleTest 7: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 7: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (0 ms) 7: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 7: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (1 ms) 7: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 7: [ OK ] CommandLineHelpModuleTest.ExportsHelp (1 ms) 7: [----------] 3 tests from CommandLineHelpModuleTest (2 ms total) 7: 7: [----------] 7 tests from CommandLineHelpWriterTest 7: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 7: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (0 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 7: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 7: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 7: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (1 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 7: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 7: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) 7: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues 7: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms) 7: [----------] 7 tests from CommandLineHelpWriterTest (1 ms total) 7: 7: [----------] 6 tests from CommandLineModuleManagerTest 7: [ RUN ] CommandLineModuleManagerTest.RunsModule 7: [ OK ] CommandLineModuleManagerTest.RunsModule (12 ms) 7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (1 ms) 7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 7: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 7: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 7: [----------] 6 tests from CommandLineModuleManagerTest (13 ms total) 7: 7: [----------] 13 tests from CommandLineParserTest 7: [ RUN ] CommandLineParserTest.HandlesSingleValues 7: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 7: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 7: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 7: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 7: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 7: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesString 7: [ OK ] CommandLineParserTest.HandlesString (0 ms) 7: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 7: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 7: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 7: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 7: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 7: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 7: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 7: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 7: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 7: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 7: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 7: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 7: [----------] 13 tests from CommandLineParserTest (0 ms total) 7: 7: [----------] 6 tests from CommandLineProgramContextTest 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 7: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 7: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (20 ms) 7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 7: [----------] 6 tests from CommandLineProgramContextTest (20 ms total) 7: 7: [----------] 3 tests from OutputNamesTest 7: [ RUN ] OutputNamesTest.CanBeSuffixed 7: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) 7: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend 7: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) 7: [ RUN ] OutputNamesTest.CanHavePartNumberAdded 7: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms) 7: [----------] 3 tests from OutputNamesTest (0 ms total) 7: 7: [----------] 21 tests from ParseCommonArgsTest 7: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 7: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 7: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 7: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 7: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 7: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 7: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 7: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 7: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 7: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 7: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 7: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 7: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 7: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 7: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 7: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 7: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 7: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 7: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 7: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 7: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 7: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 7: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (16 ms) 7: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 7: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 7: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 7: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (1 ms) 7: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 7: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (0 ms) 7: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 7: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 7: [----------] 21 tests from ParseCommonArgsTest (17 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 59 tests from 7 test cases ran. (53 ms total) 7: [ PASSED ] 59 tests. 7/30 Test #7: CommandLineUnitTests ............. Passed 0.58 sec test 8 Start 8: DomDecTests 8: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/bin/domdec-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/Testing/Temporary/DomDecTests.xml" 8: Test timeout computed to be: 30 8: [==========] Running 9 tests from 2 test cases. 8: [----------] Global test environment set-up. 8: [----------] 7 tests from HashedMap 8: [ RUN ] HashedMap.InsertsFinds 8: [ OK ] HashedMap.InsertsFinds (0 ms) 8: [ RUN ] HashedMap.NegativeKeysWork 8: [ OK ] HashedMap.NegativeKeysWork (0 ms) 8: [ RUN ] HashedMap.InsertsErases 8: [ OK ] HashedMap.InsertsErases (0 ms) 8: [ RUN ] HashedMap.InsertsOrAssigns 8: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 8: [ RUN ] HashedMap.Clears 8: [ OK ] HashedMap.Clears (0 ms) 8: [ RUN ] HashedMap.LinkedEntries 8: [ OK ] HashedMap.LinkedEntries (0 ms) 8: [ RUN ] HashedMap.ResizesTable 8: [ OK ] HashedMap.ResizesTable (0 ms) 8: [----------] 7 tests from HashedMap (0 ms total) 8: 8: [----------] 2 tests from LocalAtomSetManager 8: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 8: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 8: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 8: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 8: [----------] 2 tests from LocalAtomSetManager (0 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 9 tests from 2 test cases ran. (1 ms total) 8: [ PASSED ] 9 tests. 8/30 Test #8: DomDecTests ...................... Passed 0.61 sec test 9 Start 9: EwaldUnitTests 9: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/bin/ewald-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/Testing/Temporary/EwaldUnitTests.xml" 9: Test timeout computed to be: 30 9: [==========] Running 257 tests from 10 test cases. 9: [----------] Global test environment set-up. 9: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (1 ms) 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (3 ms) 9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 9: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (4 ms total) 9: 9: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (2 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (0 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (0 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (4 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (1 ms) 9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (1 ms) 9: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (27 ms total) 9: 9: [----------] 144 tests from SaneInput/PmeGatherTest 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (9 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/72 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/72 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/73 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/73 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/74 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/74 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/75 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/75 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/76 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/76 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/77 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/77 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/78 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/78 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/79 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/79 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/80 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/80 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/81 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/81 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/82 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/82 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/83 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/83 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/84 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/84 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/85 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/85 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/86 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/86 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/87 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/87 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/88 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/88 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/89 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/89 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/90 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/90 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/91 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/91 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/92 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/92 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/93 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/93 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/94 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/94 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/95 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/95 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/96 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/96 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/97 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/97 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/98 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/98 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/99 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/99 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/100 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/100 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/101 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/101 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/102 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/102 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/103 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/103 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/104 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/104 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/105 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/105 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/106 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/106 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/107 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/107 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/108 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/108 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/109 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/109 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/110 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/110 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/111 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/111 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/112 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/112 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/113 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/113 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/114 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/114 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/115 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/115 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/116 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/116 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/117 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/117 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/118 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/118 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/119 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/119 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/120 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/120 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/121 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/121 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/122 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/122 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/123 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/123 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/124 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/124 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/125 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/125 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/126 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/126 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/127 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/127 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/128 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/128 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/129 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/129 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/130 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/130 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/131 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/131 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/132 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/132 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/133 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/133 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/134 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/134 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/135 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/135 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/136 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/136 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/137 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/137 (12 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/138 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/138 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/139 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/139 (1 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/140 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/140 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/141 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/141 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/142 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/142 (0 ms) 9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/143 9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/143 (1 ms) 9: [----------] 144 tests from SaneInput/PmeGatherTest (69 ms total) 9: 9: [----------] 16 tests from SaneInput/PmeSolveTest 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (2 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (2 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (2 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (0 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (2 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (0 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (2 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (0 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (1 ms) 9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15 9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (1 ms) 9: [----------] 16 tests from SaneInput/PmeSolveTest (19 ms total) 9: 9: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (0 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (1 ms) 9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (0 ms) 9: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (6 ms total) 9: 9: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (2 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (1 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (1 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (1 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (1 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (1 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (1 ms) 9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (1 ms) 9: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (9 ms total) 9: 9: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (0 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (1 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (0 ms) 9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (2 ms) 9: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (15 ms total) 9: 9: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (1 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (16 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (1 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (2 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (1 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (2 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (0 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (1 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (1 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (1 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (1 ms) 9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (1 ms) 9: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (29 ms total) 9: 9: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (2 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (2 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (1 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (2 ms) 9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (2 ms) 9: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (16 ms total) 9: 9: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (2 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (2 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (4 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (4 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (6 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (5 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (3 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (2 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (3 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (3 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (4 ms) 9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (34 ms) 9: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (73 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 257 tests from 10 test cases ran. (318 ms total) 9: [ PASSED ] 257 tests. 9/30 Test #9: EwaldUnitTests ................... Passed 0.84 sec test 10 Start 10: FFTUnitTests 10: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/bin/fft-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/Testing/Temporary/FFTUnitTests.xml" 10: Test timeout computed to be: 30 10: [==========] Running 14 tests from 4 test cases. 10: [----------] Global test environment set-up. 10: [----------] 2 tests from ManyFFTTest 10: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 10: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (7 ms) 10: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 10: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (25 ms) 10: [----------] 2 tests from ManyFFTTest (34 ms total) 10: 10: [----------] 1 test from FFTTest 10: [ RUN ] FFTTest.Real2DLength18_15Test 10: [ OK ] FFTTest.Real2DLength18_15Test (7 ms) 10: [----------] 1 test from FFTTest (8 ms total) 10: 10: [----------] 1 test from FFFTest3D 10: [ RUN ] FFFTest3D.Real5_6_9 10: [ OK ] FFFTest3D.Real5_6_9 (1 ms) 10: [----------] 1 test from FFFTest3D (1 ms total) 10: 10: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (1 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (1 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (1 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (4 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (2 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (0 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (1 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (1 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (18 ms) 10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (24 ms) 10: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (54 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 14 tests from 4 test cases ran. (97 ms total) 10: [ PASSED ] 14 tests. 10/30 Test #10: FFTUnitTests ..................... Passed 0.62 sec test 11 Start 11: GpuUtilsUnitTests 11: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/bin/gpu_utils-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/Testing/Temporary/GpuUtilsUnitTests.xml" 11: Test timeout computed to be: 30 11: [==========] Running 62 tests from 20 test cases. 11: [----------] Global test environment set-up. 11: [----------] 2 tests from ClfftInitializer 11: [ RUN ] ClfftInitializer.SingleInitializationWorks 11: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) 11: [ RUN ] ClfftInitializer.TwoInitializationsWork 11: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) 11: [----------] 2 tests from ClfftInitializer (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 11: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 11: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 11: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 11: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float 11: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 11: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 11: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 11: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 11: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 11: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 11: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 11: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 11: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 11: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 11: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 11: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 11: 11: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 11: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 11: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 11: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 11: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 11: [----------] 3 tests from HostAllocatorTestCopyable/0 (1 ms total) 11: 11: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float 11: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 11: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 11: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 11: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 11: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 11: 11: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 11: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 11: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 11: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 11: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 11: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 11: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 11: 11: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 11: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 11: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 11: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 11: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/0.Swap 11: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/0.Comparison 11: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 11: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 11: 11: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float 11: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 11: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 11: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 11: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/1.Swap 11: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/1.Comparison 11: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 11: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 11: 11: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 11: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 11: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 11: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 11: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/2.Swap 11: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/2.Comparison 11: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 11: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 11: 11: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 11: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 11: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 11: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 11: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/3.Swap 11: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 11: [ RUN ] HostAllocatorTestNoMem/3.Comparison 11: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 11: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 11: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 11: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 11: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float 11: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 11: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 11: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 11: 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 11: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 11: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 11: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 11: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 11: 11: [----------] 1 test from HostAllocatorUntypedTest 11: [ RUN ] HostAllocatorUntypedTest.Comparison 11: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 11: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 11: 11: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 11: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/0.Move 11: [ OK ] AllocatorTest/0.Move (0 ms) 11: [----------] 4 tests from AllocatorTest/0 (0 ms total) 11: 11: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 11: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/1.Move 11: [ OK ] AllocatorTest/1.Move (0 ms) 11: [----------] 4 tests from AllocatorTest/1 (0 ms total) 11: 11: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 11: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/2.Move 11: [ OK ] AllocatorTest/2.Move (0 ms) 11: [----------] 4 tests from AllocatorTest/2 (0 ms total) 11: 11: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 11: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/3.Move 11: [ OK ] AllocatorTest/3.Move (0 ms) 11: [----------] 4 tests from AllocatorTest/3 (0 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 62 tests from 20 test cases ran. (1 ms total) 11: [ PASSED ] 62 tests. 11/30 Test #11: GpuUtilsUnitTests ................ Passed 0.54 sec test 12 Start 12: HardwareUnitTests 12: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/bin/hardware-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/Testing/Temporary/HardwareUnitTests.xml" 12: Test timeout computed to be: 30 12: [==========] Running 4 tests from 1 test case. 12: [----------] Global test environment set-up. 12: [----------] 4 tests from HardwareTopologyTest 12: [ RUN ] HardwareTopologyTest.Execute 12: [ OK ] HardwareTopologyTest.Execute (40 ms) 12: [ RUN ] HardwareTopologyTest.HwlocExecute 12: [ OK ] HardwareTopologyTest.HwlocExecute (49 ms) 12: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 12: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (38 ms) 12: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 12: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (33 ms) 12: [----------] 4 tests from HardwareTopologyTest (160 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 4 tests from 1 test case ran. (161 ms total) 12: [ PASSED ] 4 tests. 12/30 Test #12: HardwareUnitTests ................ Passed 0.70 sec test 13 Start 13: MathUnitTests 13: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/bin/math-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/Testing/Temporary/MathUnitTests.xml" 13: Test timeout computed to be: 30 13: [==========] Running 204 tests from 29 test cases. 13: [----------] Global test environment set-up. 13: [----------] 1 test from EmptyArrayRefWithPaddingTest 13: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 13: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 13: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 13: 13: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 13: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 13: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 13: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 13: 13: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 13: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 13: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 13: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 13: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 13: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 13: 13: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 13: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 13: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 13: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 13: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 13: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 13: 13: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 13: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 13: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 13: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 13: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 13: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 13: 13: [----------] 8 tests from TranslateAndScaleTest 13: [ RUN ] TranslateAndScaleTest.identityTransformation 13: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms) 13: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling 13: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) 13: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation 13: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) 13: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial 13: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (1 ms) 13: [ RUN ] TranslateAndScaleTest.scalingIdentity 13: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms) 13: [ RUN ] TranslateAndScaleTest.scalingNonTrivial 13: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) 13: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero 13: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms) 13: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero 13: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) 13: [----------] 8 tests from TranslateAndScaleTest (1 ms total) 13: 13: [----------] 12 tests from DensitySimilarityTest 13: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect 13: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect 13: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch 13: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms) 13: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch 13: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms) 13: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect 13: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero 13: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms) 13: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect 13: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect 13: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms) 13: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne 13: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (40 ms) 13: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated 13: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (35 ms) 13: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated 13: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (26 ms) 13: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect 13: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms) 13: [----------] 12 tests from DensitySimilarityTest (101 ms total) 13: 13: [----------] 6 tests from StructureSimilarityTest 13: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 13: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 13: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 13: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 13: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 13: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 13: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 13: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 13: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 13: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 13: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 13: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 13: [----------] 6 tests from StructureSimilarityTest (0 ms total) 13: 13: [----------] 8 tests from ExponentialMovingAverage 13: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero 13: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) 13: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative 13: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) 13: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue 13: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) 13: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue 13: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) 13: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly 13: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) 13: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing 13: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) 13: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect 13: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) 13: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree 13: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) 13: [----------] 8 tests from ExponentialMovingAverage (0 ms total) 13: 13: [----------] 21 tests from FunctionTest 13: [ RUN ] FunctionTest.StaticLog2 13: [ OK ] FunctionTest.StaticLog2 (0 ms) 13: [ RUN ] FunctionTest.Log2I32Bit 13: [ OK ] FunctionTest.Log2I32Bit (0 ms) 13: [ RUN ] FunctionTest.Log2I64Bit 13: [ OK ] FunctionTest.Log2I64Bit (1 ms) 13: [ RUN ] FunctionTest.GreatestCommonDivisor 13: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 13: [ RUN ] FunctionTest.InvsqrtFloat 13: [ OK ] FunctionTest.InvsqrtFloat (0 ms) 13: [ RUN ] FunctionTest.InvsqrtDouble 13: [ OK ] FunctionTest.InvsqrtDouble (0 ms) 13: [ RUN ] FunctionTest.InvsqrtInteger 13: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 13: [ RUN ] FunctionTest.InvcbrtFloat 13: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 13: [ RUN ] FunctionTest.InvcbrtDouble 13: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 13: [ RUN ] FunctionTest.InvcbrtInteger 13: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 13: [ RUN ] FunctionTest.SixthrootFloat 13: [ OK ] FunctionTest.SixthrootFloat (0 ms) 13: [ RUN ] FunctionTest.SixthrootDouble 13: [ OK ] FunctionTest.SixthrootDouble (1 ms) 13: [ RUN ] FunctionTest.SixthrootInteger 13: [ OK ] FunctionTest.SixthrootInteger (0 ms) 13: [ RUN ] FunctionTest.InvsixthrootFloat 13: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 13: [ RUN ] FunctionTest.InvsixthrootDouble 13: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 13: [ RUN ] FunctionTest.InvsixthrootInteger 13: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 13: [ RUN ] FunctionTest.Powers 13: [ OK ] FunctionTest.Powers (0 ms) 13: [ RUN ] FunctionTest.ErfInvFloat 13: [ OK ] FunctionTest.ErfInvFloat (19 ms) 13: [ RUN ] FunctionTest.ErfInvDouble 13: [ OK ] FunctionTest.ErfInvDouble (0 ms) 13: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 13: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 13: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 13: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (1 ms) 13: [----------] 21 tests from FunctionTest (22 ms total) 13: 13: [----------] 4 tests from GaussianOn1DLattice 13: [ RUN ] GaussianOn1DLattice.sumsCloseToOne 13: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) 13: [ RUN ] GaussianOn1DLattice.isCorrect 13: [ OK ] GaussianOn1DLattice.isCorrect (0 ms) 13: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero 13: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) 13: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange 13: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) 13: [----------] 4 tests from GaussianOn1DLattice (0 ms total) 13: 13: [----------] 9 tests from GaussTransformTest 13: [ RUN ] GaussTransformTest.isZeroUponConstruction 13: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) 13: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss 13: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) 13: [ RUN ] GaussTransformTest.isZeroAfterSettingZero 13: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) 13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX 13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) 13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY 13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) 13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ 13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) 13: [ RUN ] GaussTransformTest.complementaryGaussAddToZero 13: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) 13: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues 13: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms) 13: [ RUN ] GaussTransformTest.view 13: [ OK ] GaussTransformTest.view (0 ms) 13: [----------] 9 tests from GaussTransformTest (0 ms total) 13: 13: [----------] 3 tests from DensityFittingForce 13: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity 13: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) 13: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections 13: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) 13: [ RUN ] DensityFittingForce.pullsTowardsDerivative 13: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) 13: [----------] 3 tests from DensityFittingForce (0 ms total) 13: 13: [----------] 2 tests from InvertMatrixTest 13: [ RUN ] InvertMatrixTest.IdentityIsImpotent 13: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 13: [ RUN ] InvertMatrixTest.ComputesInverse 13: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 13: [----------] 2 tests from InvertMatrixTest (0 ms total) 13: 13: [----------] 2 tests from InvertBoxMatrixTest 13: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 13: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 13: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 13: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 13: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 13: 13: [----------] 15 tests from MatrixTest 13: [ RUN ] MatrixTest.canSetFromArray 13: [ OK ] MatrixTest.canSetFromArray (0 ms) 13: [ RUN ] MatrixTest.canSetStaticallyFromList 13: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) 13: [ RUN ] MatrixTest.canConstructAndFill 13: [ OK ] MatrixTest.canConstructAndFill (0 ms) 13: [ RUN ] MatrixTest.canSetValues 13: [ OK ] MatrixTest.canSetValues (0 ms) 13: [ RUN ] MatrixTest.canCopyAssign 13: [ OK ] MatrixTest.canCopyAssign (0 ms) 13: [ RUN ] MatrixTest.canSwap 13: [ OK ] MatrixTest.canSwap (0 ms) 13: [ RUN ] MatrixTest.staticMultiDimArrayExtent 13: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) 13: [ RUN ] MatrixTest.determinantWorks 13: [ OK ] MatrixTest.determinantWorks (0 ms) 13: [ RUN ] MatrixTest.noninvertableDeterminantIsZero 13: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) 13: [ RUN ] MatrixTest.determinantOfDiagonalMatrix 13: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) 13: [ RUN ] MatrixTest.traceWorks 13: [ OK ] MatrixTest.traceWorks (0 ms) 13: [ RUN ] MatrixTest.transposeWorks 13: [ OK ] MatrixTest.transposeWorks (0 ms) 13: [ RUN ] MatrixTest.transposeOfSymmetricMatrix 13: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) 13: [ RUN ] MatrixTest.canCreateFromLegacyMatrix 13: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) 13: [ RUN ] MatrixTest.canFillLegacyMatrix 13: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) 13: [----------] 15 tests from MatrixTest (0 ms total) 13: 13: [----------] 25 tests from MultiDimArrayTest 13: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic 13: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic 13: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canSetValuesInStatic 13: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic 13: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canMoveConstructStatic 13: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic 13: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canMoveAssignStatic 13: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic 13: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canCopyConstructStatic 13: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic 13: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canCopyAssignStatic 13: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic 13: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.canSwapStatic 13: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) 13: [ RUN ] MultiDimArrayTest.canSwapDynamic 13: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) 13: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent 13: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) 13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent 13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) 13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent 13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) 13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue 13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) 13: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray 13: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) 13: [ RUN ] MultiDimArrayTest.conversionToView 13: [ OK ] MultiDimArrayTest.conversionToView (0 ms) 13: [ RUN ] MultiDimArrayTest.conversionToConstView 13: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) 13: [ RUN ] MultiDimArrayTest.viewBegin 13: [ OK ] MultiDimArrayTest.viewBegin (0 ms) 13: [ RUN ] MultiDimArrayTest.viewEnd 13: [ OK ] MultiDimArrayTest.viewEnd (0 ms) 13: [ RUN ] MultiDimArrayTest.constViewConstBegin 13: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) 13: [ RUN ] MultiDimArrayTest.constViewConstEnd 13: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) 13: [----------] 25 tests from MultiDimArrayTest (1 ms total) 13: 13: [----------] 4 tests from MultiDimArrayToMdSpanTest 13: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan 13: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) 13: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan 13: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) 13: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan 13: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) 13: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan 13: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) 13: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/0, where TypeParam = std::allocator 13: [ RUN ] PaddedVectorTest/0.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/0.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/0.CanCopyAssign 13: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/0.CanMoveAssign 13: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/0.CanSwap 13: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/0 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/1, where TypeParam = std::allocator 13: [ RUN ] PaddedVectorTest/1.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/1.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/1.CanCopyAssign 13: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/1.CanMoveAssign 13: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/1.CanSwap 13: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/1 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/2, where TypeParam = std::allocator 13: [ RUN ] PaddedVectorTest/2.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/2.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/2.CanCopyAssign 13: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/2.CanMoveAssign 13: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/2.CanSwap 13: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/2 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 13: [ RUN ] PaddedVectorTest/3.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/3.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/3.CanCopyAssign 13: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/3.CanMoveAssign 13: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/3.CanSwap 13: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/3 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 13: [ RUN ] PaddedVectorTest/4.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/4.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/4.CanCopyAssign 13: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/4.CanMoveAssign 13: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/4.CanSwap 13: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/4 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 13: [ RUN ] PaddedVectorTest/5.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/5.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/5.CanCopyAssign 13: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/5.CanMoveAssign 13: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/5.CanSwap 13: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/5 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 13: [ RUN ] PaddedVectorTest/6.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/6.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/6.CanCopyAssign 13: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/6.CanMoveAssign 13: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/6.CanSwap 13: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/6 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 13: [ RUN ] PaddedVectorTest/7.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/7.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/7.CanCopyAssign 13: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/7.CanMoveAssign 13: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/7.CanSwap 13: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/7 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 13: [ RUN ] PaddedVectorTest/8.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/8.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/8.CanCopyAssign 13: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/8.CanMoveAssign 13: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/8.CanSwap 13: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/8 (0 ms total) 13: 13: [----------] 4 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 13: [ RUN ] PaddedVectorTest/9.ConstructsResizesAndReserves 13: [ OK ] PaddedVectorTest/9.ConstructsResizesAndReserves (0 ms) 13: [ RUN ] PaddedVectorTest/9.CanCopyAssign 13: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 13: [ RUN ] PaddedVectorTest/9.CanMoveAssign 13: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 13: [ RUN ] PaddedVectorTest/9.CanSwap 13: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 13: [----------] 4 tests from PaddedVectorTest/9 (0 ms total) 13: 13: [----------] 37 tests from RVecTest 13: [ RUN ] RVecTest.CanBeStoredInVector 13: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 13: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 13: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 13: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 13: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 13: [ RUN ] RVecTest.WorksAsMutable_rvec 13: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 13: [ RUN ] RVecTest.WorksAs_rvec_Array 13: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 13: [ RUN ] RVecTest.CanAddRVecToRvec 13: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 13: [ RUN ] RVecTest.CanAddAssignRVecToRvec 13: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 13: [ RUN ] RVecTest.CanSubtractRVecFromRvec 13: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 13: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 13: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 13: [ RUN ] RVecTest.CanDotProductRVecByRvec 13: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 13: [ RUN ] RVecTest.CanCrossProductRVecByRvec 13: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 13: [ RUN ] RVecTest.CanDivideRVecInplace 13: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 13: [ RUN ] RVecTest.CanScaleRVec 13: [ OK ] RVecTest.CanScaleRVec (0 ms) 13: [ RUN ] RVecTest.CanDivideRVec 13: [ OK ] RVecTest.CanDivideRVec (0 ms) 13: [ RUN ] RVecTest.CanDoUnitvFromRVec 13: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 13: [ RUN ] RVecTest.CanSqLengthOfRVec 13: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 13: [ RUN ] RVecTest.CanLengthOfRVec 13: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 13: [ RUN ] RVecTest.CanCastToRVec 13: [ OK ] RVecTest.CanCastToRVec (0 ms) 13: [ RUN ] RVecTest.CanCastToDVec 13: [ OK ] RVecTest.CanCastToDVec (0 ms) 13: [ RUN ] RVecTest.CanLeftScalarMultiply 13: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 13: [ RUN ] RVecTest.CanRightScalarMultiply 13: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 13: [ RUN ] RVecTest.CanGetUnitvFromRVec 13: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 13: [ RUN ] RVecTest.CanGetSqLengthOfRVec 13: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 13: [ RUN ] RVecTest.CanGetLengthOfRVec 13: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 13: [ RUN ] RVecTest.CanDoCrossProductOfRVec 13: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 13: [ RUN ] RVecTest.CanDoDotProductOfRVec 13: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 13: [ RUN ] RVecTest.CanScaleByVector 13: [ OK ] RVecTest.CanScaleByVector (0 ms) 13: [ RUN ] RVecTest.asIVec 13: [ OK ] RVecTest.asIVec (0 ms) 13: [ RUN ] RVecTest.elementWiseMin 13: [ OK ] RVecTest.elementWiseMin (0 ms) 13: [ RUN ] RVecTest.elementWiseMax 13: [ OK ] RVecTest.elementWiseMax (0 ms) 13: [ RUN ] RVecTest.WorksAs_dvec_Reference 13: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 13: [ RUN ] RVecTest.WorksAs_ivec_Reference 13: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 13: [ RUN ] RVecTest.WorksAs_rvec_Reference 13: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 13: [ RUN ] RVecTest.CopyConstructorWorks 13: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 13: [ RUN ] RVecTest.CopyAssignmentWorks 13: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 13: [ RUN ] RVecTest.MoveConstructorWorks 13: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 13: [ RUN ] RVecTest.MoveAssignmentWorks 13: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 13: [----------] 37 tests from RVecTest (1 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 204 tests from 29 test cases ran. (126 ms total) 13: [ PASSED ] 204 tests. 13/30 Test #13: MathUnitTests .................... Passed 0.61 sec test 14 Start 14: MdrunUtilityUnitTests 14: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/bin/mdrunutility-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/Testing/Temporary/MdrunUtilityUnitTests.xml" 14: Test timeout computed to be: 30 14: [==========] Running 17 tests from 1 test case. 14: [----------] Global test environment set-up. 14: [----------] 17 tests from ThreadAffinityTest 14: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 14: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 14: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 14: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (1 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 14: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 14: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 14: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 14: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) 14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 14: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 14: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (0 ms) 14: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 14: NOTE: Affinity setting failed. 14: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (1 ms) 14: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 14: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (0 ms) 14: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 14: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (0 ms) 14: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 14: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (0 ms) 14: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 14: NOTE: Affinity setting for 1/2 threads failed. 14: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (0 ms) 14: [----------] 17 tests from ThreadAffinityTest (2 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 17 tests from 1 test case ran. (2 ms total) 14: [ PASSED ] 17 tests. 14/30 Test #14: MdrunUtilityUnitTests ............ Passed 0.52 sec test 15 Start 15: MdrunUtilityMpiUnitTests 15: Test command: /usr/bin/mpiexec.openmpi "-np" "4" "-host" "localhost" "/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/bin/mdrunutility-mpi-test" "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 15: Test timeout computed to be: 30 15: [==========] Running 13 tests from 2 test cases. 15: [----------] Global test environment set-up. 15: [----------] 6 tests from ThreadAffinityMultiRankTest 15: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 15: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (0 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 15: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (1 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 15: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (0 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 15: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (1 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 15: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (0 ms) 15: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 15: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (0 ms) 15: [----------] 6 tests from ThreadAffinityMultiRankTest (2 ms total) 15: 15: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (0 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (0 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (0 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (1 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (0 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (35 ms) 15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly 15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (1 ms) 15: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (38 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 13 tests from 2 test cases ran. (41 ms total) 15: [ PASSED ] 13 tests. 15/30 Test #15: MdrunUtilityMpiUnitTests ......... Passed 0.80 sec test 16 Start 16: MDSpanTests 16: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/bin/mdspan-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/Testing/Temporary/MDSpanTests.xml" 16: Test timeout computed to be: 30 16: [==========] Running 32 tests from 7 test cases. 16: [----------] Global test environment set-up. 16: [----------] 4 tests from BasicAccessorPolicy 16: [ RUN ] BasicAccessorPolicy.Decay 16: [ OK ] BasicAccessorPolicy.Decay (0 ms) 16: [ RUN ] BasicAccessorPolicy.Access 16: [ OK ] BasicAccessorPolicy.Access (0 ms) 16: [ RUN ] BasicAccessorPolicy.Offset 16: [ OK ] BasicAccessorPolicy.Offset (0 ms) 16: [ RUN ] BasicAccessorPolicy.CopyAccessor 16: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) 16: [----------] 4 tests from BasicAccessorPolicy (0 ms total) 16: 16: [----------] 4 tests from ExtentsTest 16: [ RUN ] ExtentsTest.Construction 16: [ OK ] ExtentsTest.Construction (0 ms) 16: [ RUN ] ExtentsTest.PurelyStatic 16: [ OK ] ExtentsTest.PurelyStatic (0 ms) 16: [ RUN ] ExtentsTest.RankNought 16: [ OK ] ExtentsTest.RankNought (0 ms) 16: [ RUN ] ExtentsTest.Assignment 16: [ OK ] ExtentsTest.Assignment (0 ms) 16: [----------] 4 tests from ExtentsTest (0 ms total) 16: 16: [----------] 8 tests from MdSpanExtension 16: [ RUN ] MdSpanExtension.SlicingAllStatic 16: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) 16: [ RUN ] MdSpanExtension.SlicingDynamic 16: [ OK ] MdSpanExtension.SlicingDynamic (0 ms) 16: [ RUN ] MdSpanExtension.SlicingAllStatic3D 16: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) 16: [ RUN ] MdSpanExtension.SlicingEqualsView3D 16: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) 16: [ RUN ] MdSpanExtension.additionWorks 16: [ OK ] MdSpanExtension.additionWorks (0 ms) 16: [ RUN ] MdSpanExtension.subtractionWorks 16: [ OK ] MdSpanExtension.subtractionWorks (0 ms) 16: [ RUN ] MdSpanExtension.multiplicationWorks 16: [ OK ] MdSpanExtension.multiplicationWorks (0 ms) 16: [ RUN ] MdSpanExtension.divisionWorks 16: [ OK ] MdSpanExtension.divisionWorks (0 ms) 16: [----------] 8 tests from MdSpanExtension (0 ms total) 16: 16: [----------] 3 tests from LayoutTests 16: [ RUN ] LayoutTests.LayoutRightConstruction 16: [ OK ] LayoutTests.LayoutRightConstruction (0 ms) 16: [ RUN ] LayoutTests.LayoutRightProperties 16: [ OK ] LayoutTests.LayoutRightProperties (0 ms) 16: [ RUN ] LayoutTests.LayoutRightOperator 16: [ OK ] LayoutTests.LayoutRightOperator (0 ms) 16: [----------] 3 tests from LayoutTests (0 ms total) 16: 16: [----------] 1 test from MdSpanTest 16: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly 16: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) 16: [----------] 1 test from MdSpanTest (0 ms total) 16: 16: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 16: [ RUN ] MdSpanTest/0.Rank 16: [ OK ] MdSpanTest/0.Rank (0 ms) 16: [ RUN ] MdSpanTest/0.DynamicRank 16: [ OK ] MdSpanTest/0.DynamicRank (0 ms) 16: [ RUN ] MdSpanTest/0.Extents 16: [ OK ] MdSpanTest/0.Extents (0 ms) 16: [ RUN ] MdSpanTest/0.Strides 16: [ OK ] MdSpanTest/0.Strides (0 ms) 16: [ RUN ] MdSpanTest/0.Properties 16: [ OK ] MdSpanTest/0.Properties (0 ms) 16: [ RUN ] MdSpanTest/0.Operator 16: [ OK ] MdSpanTest/0.Operator (0 ms) 16: [----------] 6 tests from MdSpanTest/0 (0 ms total) 16: 16: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 16: [ RUN ] MdSpanTest/1.Rank 16: [ OK ] MdSpanTest/1.Rank (0 ms) 16: [ RUN ] MdSpanTest/1.DynamicRank 16: [ OK ] MdSpanTest/1.DynamicRank (0 ms) 16: [ RUN ] MdSpanTest/1.Extents 16: [ OK ] MdSpanTest/1.Extents (0 ms) 16: [ RUN ] MdSpanTest/1.Strides 16: [ OK ] MdSpanTest/1.Strides (0 ms) 16: [ RUN ] MdSpanTest/1.Properties 16: [ OK ] MdSpanTest/1.Properties (0 ms) 16: [ RUN ] MdSpanTest/1.Operator 16: [ OK ] MdSpanTest/1.Operator (0 ms) 16: [----------] 6 tests from MdSpanTest/1 (0 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 32 tests from 7 test cases ran. (1 ms total) 16: [ PASSED ] 32 tests. 16/30 Test #16: MDSpanTests ...................... Passed 0.54 sec test 17 Start 17: OnlineHelpUnitTests 17: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/bin/onlinehelp-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/Testing/Temporary/OnlineHelpUnitTests.xml" 17: Test timeout computed to be: 30 17: [==========] Running 22 tests from 4 test cases. 17: [----------] Global test environment set-up. 17: [----------] 6 tests from TextTableFormatterTest 17: [ RUN ] TextTableFormatterTest.HandlesBasicCase 17: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms) 17: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 17: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) 17: [ RUN ] TextTableFormatterTest.HandlesIndentation 17: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) 17: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 17: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) 17: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 17: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms) 17: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 17: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) 17: [----------] 6 tests from TextTableFormatterTest (1 ms total) 17: 17: [----------] 3 tests from HelpManagerTest 17: [ RUN ] HelpManagerTest.HandlesRootTopic 17: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 17: [ RUN ] HelpManagerTest.HandlesSubTopics 17: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 17: [ RUN ] HelpManagerTest.HandlesInvalidTopics 17: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 17: [----------] 3 tests from HelpManagerTest (0 ms total) 17: 17: [----------] 2 tests from HelpTopicFormattingTest 17: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 17: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms) 17: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 17: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) 17: [----------] 2 tests from HelpTopicFormattingTest (0 ms total) 17: 17: [----------] 11 tests from HelpWriterContextTest 17: [ RUN ] HelpWriterContextTest.FormatsParagraphs 17: [ OK ] HelpWriterContextTest.FormatsParagraphs (4 ms) 17: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 17: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 17: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 17: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsLiteralText 17: [ OK ] HelpWriterContextTest.FormatsLiteralText (1 ms) 17: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 17: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 17: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsBulletList 17: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 17: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 17: [ OK ] HelpWriterContextTest.FormatsSimpleTable (1 ms) 17: [ RUN ] HelpWriterContextTest.FormatsGridTable 17: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms) 17: [ RUN ] HelpWriterContextTest.FormatsTitles 17: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) 17: [----------] 11 tests from HelpWriterContextTest (6 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 22 tests from 4 test cases ran. (7 ms total) 17: [ PASSED ] 22 tests. 17/30 Test #17: OnlineHelpUnitTests .............. Passed 0.54 sec test 18 Start 18: OptionsUnitTests 18: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/bin/options-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/Testing/Temporary/OptionsUnitTests.xml" 18: Test timeout computed to be: 30 18: [==========] Running 110 tests from 18 test cases. 18: [----------] Global test environment set-up. 18: [----------] 5 tests from AbstractOptionStorageTest 18: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 18: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 18: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 18: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) 18: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 18: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 18: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 18: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (1 ms) 18: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 18: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 18: [----------] 5 tests from AbstractOptionStorageTest (1 ms total) 18: 18: [----------] 8 tests from FileNameOptionTest 18: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 18: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 18: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 18: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 18: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 18: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 18: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 18: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 18: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 18: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 18: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 18: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 18: [----------] 8 tests from FileNameOptionTest (0 ms total) 18: 18: [----------] 15 tests from FileNameOptionManagerTest 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 18: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 18: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 18: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 18: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 18: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 18: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 18: [----------] 15 tests from FileNameOptionManagerTest (1 ms total) 18: 18: [----------] 1 test from OptionsTest 18: [ RUN ] OptionsTest.FailsOnNonsafeStorage 18: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 18: [----------] 1 test from OptionsTest (0 ms total) 18: 18: [----------] 9 tests from OptionsAssignerTest 18: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 18: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 18: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 18: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 18: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesMissingValue 18: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesExtraValue 18: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesGroups 18: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesSections 18: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 18: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 18: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 18: [----------] 9 tests from OptionsAssignerTest (0 ms total) 18: 18: [----------] 4 tests from OptionsAssignerBooleanTest 18: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 18: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 18: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 18: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 18: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 18: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 18: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 18: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 18: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 18: 18: [----------] 13 tests from OptionsAssignerIntegerTest 18: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 18: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 18: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 18: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 18: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (1 ms) 18: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 18: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 18: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 18: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 18: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 18: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 18: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 18: [----------] 13 tests from OptionsAssignerIntegerTest (1 ms total) 18: 18: [----------] 5 tests from OptionsAssignerDoubleTest 18: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 18: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 18: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 18: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 18: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 18: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 18: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 18: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 18: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 18: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 18: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 18: 18: [----------] 9 tests from OptionsAssignerStringTest 18: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 18: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 18: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 18: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 18: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 18: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 18: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 18: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 18: 18: [----------] 6 tests from OptionsAssignerEnumTest 18: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 18: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 18: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 18: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 18: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 18: 18: [----------] 8 tests from RepeatingOptionSectionTest 18: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 18: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 18: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 18: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 18: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 18: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 18: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 18: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 18: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 18: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 18: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 18: 18: [----------] 1 test from TimeUnitManagerTest 18: [ RUN ] TimeUnitManagerTest.BasicOperations 18: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 18: [----------] 1 test from TimeUnitManagerTest (0 ms total) 18: 18: [----------] 4 tests from TimeUnitBehaviorTest 18: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 18: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 18: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 18: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 18: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 18: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 18: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 18: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 18: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 18: 18: [----------] 2 tests from TreeValueSupportAssignTest 18: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 18: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 18: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 18: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 18: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) 18: 18: [----------] 1 test from TreeValueSupportAssignErrorTest 18: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 18: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 18: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 18: 18: [----------] 5 tests from TreeValueSupportCheckTest 18: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 18: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 18: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 18: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 18: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 18: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 18: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 18: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 18: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 18: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 18: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 18: 18: [----------] 6 tests from TreeValueSupportAdjustTest 18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms) 18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) 18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (1 ms) 18: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 18: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 18: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 18: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) 18: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 18: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 18: [----------] 6 tests from TreeValueSupportAdjustTest (1 ms total) 18: 18: [----------] 8 tests from TreeValueSupportTest 18: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 18: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 18: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsInt64Option 18: [ OK ] TreeValueSupportTest.SupportsInt64Option (1 ms) 18: [ RUN ] TreeValueSupportTest.SupportsStringOption 18: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsFloatOption 18: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 18: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsEnumIntOption 18: [ OK ] TreeValueSupportTest.SupportsEnumIntOption (0 ms) 18: [ RUN ] TreeValueSupportTest.SupportsEnumOption 18: [ OK ] TreeValueSupportTest.SupportsEnumOption (1 ms) 18: [----------] 8 tests from TreeValueSupportTest (2 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 110 tests from 18 test cases ran. (7 ms total) 18: [ PASSED ] 110 tests. 18/30 Test #18: OptionsUnitTests ................. Passed 0.48 sec test 19 Start 19: PbcutilUnitTest 19: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/bin/pbcutil-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/Testing/Temporary/PbcutilUnitTest.xml" 19: Test timeout computed to be: 30 19: [==========] Running 3 tests from 2 test cases. 19: [----------] Global test environment set-up. 19: [----------] 1 test from PbcTest 19: [ RUN ] PbcTest.CalcShiftsWorks 19: [ OK ] PbcTest.CalcShiftsWorks (1 ms) 19: [----------] 1 test from PbcTest (1 ms total) 19: 19: [----------] 2 tests from PbcEnumsTest 19: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect 19: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms) 19: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect 19: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) 19: [----------] 2 tests from PbcEnumsTest (0 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 3 tests from 2 test cases ran. (1 ms total) 19: [ PASSED ] 3 tests. 19/30 Test #19: PbcutilUnitTest .................. Passed 0.48 sec test 20 Start 20: RandomUnitTests 20: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/bin/random-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/Testing/Temporary/RandomUnitTests.xml" 20: Test timeout computed to be: 30 20: [==========] Running 44 tests from 10 test cases. 20: [----------] Global test environment set-up. 20: [----------] 4 tests from ExponentialDistributionTest 20: [ RUN ] ExponentialDistributionTest.Output 20: [ OK ] ExponentialDistributionTest.Output (0 ms) 20: [ RUN ] ExponentialDistributionTest.Logical 20: [ OK ] ExponentialDistributionTest.Logical (0 ms) 20: [ RUN ] ExponentialDistributionTest.Reset 20: [ OK ] ExponentialDistributionTest.Reset (0 ms) 20: [ RUN ] ExponentialDistributionTest.AltParam 20: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 20: [----------] 4 tests from ExponentialDistributionTest (0 ms total) 20: 20: [----------] 4 tests from GammaDistributionTest 20: [ RUN ] GammaDistributionTest.Output 20: [ OK ] GammaDistributionTest.Output (0 ms) 20: [ RUN ] GammaDistributionTest.Logical 20: [ OK ] GammaDistributionTest.Logical (0 ms) 20: [ RUN ] GammaDistributionTest.Reset 20: [ OK ] GammaDistributionTest.Reset (0 ms) 20: [ RUN ] GammaDistributionTest.AltParam 20: [ OK ] GammaDistributionTest.AltParam (0 ms) 20: [----------] 4 tests from GammaDistributionTest (0 ms total) 20: 20: [----------] 4 tests from NormalDistributionTest 20: [ RUN ] NormalDistributionTest.Output 20: [ OK ] NormalDistributionTest.Output (0 ms) 20: [ RUN ] NormalDistributionTest.Logical 20: [ OK ] NormalDistributionTest.Logical (0 ms) 20: [ RUN ] NormalDistributionTest.Reset 20: [ OK ] NormalDistributionTest.Reset (0 ms) 20: [ RUN ] NormalDistributionTest.AltParam 20: [ OK ] NormalDistributionTest.AltParam (0 ms) 20: [----------] 4 tests from NormalDistributionTest (0 ms total) 20: 20: [----------] 1 test from SeedTest 20: [ RUN ] SeedTest.makeRandomSeed 20: [ OK ] SeedTest.makeRandomSeed (0 ms) 20: [----------] 1 test from SeedTest (0 ms total) 20: 20: [----------] 6 tests from TabulatedNormalDistributionTest 20: [ RUN ] TabulatedNormalDistributionTest.Output14 20: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) 20: [ RUN ] TabulatedNormalDistributionTest.Output16 20: [ OK ] TabulatedNormalDistributionTest.Output16 (1 ms) 20: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 20: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) 20: [ RUN ] TabulatedNormalDistributionTest.Logical 20: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 20: [ RUN ] TabulatedNormalDistributionTest.Reset 20: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 20: [ RUN ] TabulatedNormalDistributionTest.AltParam 20: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 20: [----------] 6 tests from TabulatedNormalDistributionTest (1 ms total) 20: 20: [----------] 1 test from TabulatedNormalDistributionTableTest 20: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 20: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (1 ms) 20: [----------] 1 test from TabulatedNormalDistributionTableTest (1 ms total) 20: 20: [----------] 6 tests from ThreeFry2x64Test 20: [ RUN ] ThreeFry2x64Test.Logical 20: [ OK ] ThreeFry2x64Test.Logical (0 ms) 20: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 20: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) 20: [ RUN ] ThreeFry2x64Test.Reseed 20: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 20: [ RUN ] ThreeFry2x64Test.Discard 20: [ OK ] ThreeFry2x64Test.Discard (0 ms) 20: [ RUN ] ThreeFry2x64Test.InvalidCounter 20: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 20: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 20: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 20: [----------] 6 tests from ThreeFry2x64Test (0 ms total) 20: 20: [----------] 4 tests from UniformIntDistributionTest 20: [ RUN ] UniformIntDistributionTest.Output 20: [ OK ] UniformIntDistributionTest.Output (0 ms) 20: [ RUN ] UniformIntDistributionTest.Logical 20: [ OK ] UniformIntDistributionTest.Logical (0 ms) 20: [ RUN ] UniformIntDistributionTest.Reset 20: [ OK ] UniformIntDistributionTest.Reset (0 ms) 20: [ RUN ] UniformIntDistributionTest.AltParam 20: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 20: [----------] 4 tests from UniformIntDistributionTest (0 ms total) 20: 20: [----------] 5 tests from UniformRealDistributionTest 20: [ RUN ] UniformRealDistributionTest.GenerateCanonical 20: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 20: [ RUN ] UniformRealDistributionTest.Output 20: [ OK ] UniformRealDistributionTest.Output (0 ms) 20: [ RUN ] UniformRealDistributionTest.Logical 20: [ OK ] UniformRealDistributionTest.Logical (0 ms) 20: [ RUN ] UniformRealDistributionTest.Reset 20: [ OK ] UniformRealDistributionTest.Reset (0 ms) 20: [ RUN ] UniformRealDistributionTest.AltParam 20: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 20: [----------] 5 tests from UniformRealDistributionTest (1 ms total) 20: 20: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (1 ms) 20: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (1 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 44 tests from 10 test cases ran. (4 ms total) 20: [ PASSED ] 44 tests. 20/30 Test #20: RandomUnitTests .................. Passed 0.51 sec test 21 Start 21: RestraintTests 21: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/bin/restraintpotential-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/Testing/Temporary/RestraintTests.xml" 21: Test timeout computed to be: 30 21: [==========] Running 1 test from 1 test case. 21: [----------] Global test environment set-up. 21: [----------] 1 test from RestraintManager 21: [ RUN ] RestraintManager.restraintList 21: [ OK ] RestraintManager.restraintList (0 ms) 21: [----------] 1 test from RestraintManager (0 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 1 test from 1 test case ran. (0 ms total) 21: [ PASSED ] 1 test. 21/30 Test #21: RestraintTests ................... Passed 0.49 sec test 22 Start 22: TableUnitTests 22: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/bin/table-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/Testing/Temporary/TableUnitTests.xml" 22: Test timeout computed to be: 30 22: [==========] Running 20 tests from 2 test cases. 22: [----------] Global test environment set-up. 22: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 22: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 22: [ OK ] SplineTableTest/0.HandlesIncorrectInput (1 ms) 22: [ RUN ] SplineTableTest/0.Sinc 22: [ OK ] SplineTableTest/0.Sinc (1 ms) 22: [ RUN ] SplineTableTest/0.LJ12 22: [ OK ] SplineTableTest/0.LJ12 (13 ms) 22: [ RUN ] SplineTableTest/0.PmeCorrection 22: [ OK ] SplineTableTest/0.PmeCorrection (0 ms) 22: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 22: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (1 ms) 22: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 22: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (1 ms) 22: [ RUN ] SplineTableTest/0.TwoFunctions 22: [ OK ] SplineTableTest/0.TwoFunctions (27 ms) 22: [ RUN ] SplineTableTest/0.ThreeFunctions 22: [ OK ] SplineTableTest/0.ThreeFunctions (35 ms) 22: [ RUN ] SplineTableTest/0.Simd 22: [ OK ] SplineTableTest/0.Simd (7 ms) 22: [ RUN ] SplineTableTest/0.SimdTwoFunctions 22: [ OK ] SplineTableTest/0.SimdTwoFunctions (23 ms) 22: [----------] 10 tests from SplineTableTest/0 (109 ms total) 22: 22: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 22: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 22: [ OK ] SplineTableTest/1.HandlesIncorrectInput (1 ms) 22: [ RUN ] SplineTableTest/1.Sinc 22: [ OK ] SplineTableTest/1.Sinc (0 ms) 22: [ RUN ] SplineTableTest/1.LJ12 22: [ OK ] SplineTableTest/1.LJ12 (2 ms) 22: [ RUN ] SplineTableTest/1.PmeCorrection 22: [ OK ] SplineTableTest/1.PmeCorrection (1 ms) 22: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 22: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (1 ms) 22: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 22: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (1 ms) 22: [ RUN ] SplineTableTest/1.TwoFunctions 22: [ OK ] SplineTableTest/1.TwoFunctions (4 ms) 22: [ RUN ] SplineTableTest/1.ThreeFunctions 22: [ OK ] SplineTableTest/1.ThreeFunctions (4 ms) 22: [ RUN ] SplineTableTest/1.Simd 22: [ OK ] SplineTableTest/1.Simd (1 ms) 22: [ RUN ] SplineTableTest/1.SimdTwoFunctions 22: [ OK ] SplineTableTest/1.SimdTwoFunctions (3 ms) 22: [----------] 10 tests from SplineTableTest/1 (18 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 20 tests from 2 test cases ran. (127 ms total) 22: [ PASSED ] 20 tests. 22/30 Test #22: TableUnitTests ................... Passed 0.61 sec test 23 Start 23: TaskAssignmentUnitTests 23: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/bin/taskassignment-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/Testing/Temporary/TaskAssignmentUnitTests.xml" 23: Test timeout computed to be: 30 23: [==========] Running 3 tests from 2 test cases. 23: [----------] Global test environment set-up. 23: [----------] 2 tests from UserTaskAssignmentStringHandlingTest 23: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork 23: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms) 23: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid 23: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) 23: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total) 23: 23: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest 23: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow 23: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (1 ms) 23: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (1 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 3 tests from 2 test cases ran. (1 ms total) 23: [ PASSED ] 3 tests. 23/30 Test #23: TaskAssignmentUnitTests .......... Passed 0.50 sec test 24 Start 24: TopologyTest 24: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/bin/topology-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/Testing/Temporary/TopologyTest.xml" 24: Test timeout computed to be: 30 24: [==========] Running 11 tests from 3 test cases. 24: [----------] Global test environment set-up. 24: [----------] 3 tests from ExclusionBlockTest 24: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks 24: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) 24: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka 24: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) 24: [ RUN ] ExclusionBlockTest.MergeExclusions 24: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) 24: [----------] 3 tests from ExclusionBlockTest (0 ms total) 24: 24: [----------] 2 tests from MtopTest 24: [ RUN ] MtopTest.RangeBasedLoop 24: [ OK ] MtopTest.RangeBasedLoop (0 ms) 24: [ RUN ] MtopTest.Operators 24: [ OK ] MtopTest.Operators (0 ms) 24: [----------] 2 tests from MtopTest (0 ms total) 24: 24: [----------] 6 tests from SymtabTest 24: [ RUN ] SymtabTest.EmptyOnOpen 24: [ OK ] SymtabTest.EmptyOnOpen (29 ms) 24: [ RUN ] SymtabTest.AddSingleEntry 24: [ OK ] SymtabTest.AddSingleEntry (0 ms) 24: [ RUN ] SymtabTest.AddTwoDistinctEntries 24: [ OK ] SymtabTest.AddTwoDistinctEntries (0 ms) 24: [ RUN ] SymtabTest.TryToAddDuplicates 24: [ OK ] SymtabTest.TryToAddDuplicates (0 ms) 24: [ RUN ] SymtabTest.AddLargeNumberOfEntries 24: [ OK ] SymtabTest.AddLargeNumberOfEntries (0 ms) 24: [ RUN ] SymtabTest.NoDuplicatesInLargeTable 24: [ OK ] SymtabTest.NoDuplicatesInLargeTable (1 ms) 24: [----------] 6 tests from SymtabTest (30 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 11 tests from 3 test cases ran. (30 ms total) 24: [ PASSED ] 11 tests. 24/30 Test #24: TopologyTest ..................... Passed 0.58 sec test 25 Start 25: PullTest 25: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/bin/pull-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/Testing/Temporary/PullTest.xml" 25: Test timeout computed to be: 30 25: [==========] Running 5 tests from 1 test case. 25: [----------] Global test environment set-up. 25: [----------] 5 tests from PullTest 25: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 25: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 25: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 25: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 25: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 25: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 25: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 25: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 25: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 25: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 25: [----------] 5 tests from PullTest (0 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 5 tests from 1 test case ran. (0 ms total) 25: [ PASSED ] 5 tests. 25/30 Test #25: PullTest ......................... Passed 0.50 sec test 26 Start 26: AwhTest 26: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/bin/awh-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/Testing/Temporary/AwhTest.xml" 26: Test timeout computed to be: 30 26: [==========] Running 12 tests from 4 test cases. 26: [----------] Global test environment set-up. 26: [----------] 1 test from BiasTest 26: [ RUN ] BiasTest.DetectsCovering 26: [ OK ] BiasTest.DetectsCovering (1 ms) 26: [----------] 1 test from BiasTest (1 ms total) 26: 26: [----------] 1 test from gridTest 26: [ RUN ] gridTest.neighborhood 26: [ OK ] gridTest.neighborhood (2 ms) 26: [----------] 1 test from gridTest (2 ms total) 26: 26: [----------] 8 tests from WithParameters/BiasTest 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (1 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (1 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (0 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (1 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (0 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (0 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (1 ms) 26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7 26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (0 ms) 26: [----------] 8 tests from WithParameters/BiasTest (5 ms total) 26: 26: [----------] 2 tests from WithParameters/BiasStateTest 26: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 26: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (1 ms) 26: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 26: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms) 26: [----------] 2 tests from WithParameters/BiasStateTest (1 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 12 tests from 4 test cases ran. (9 ms total) 26: [ PASSED ] 12 tests. 26/30 Test #26: AwhTest .......................... Passed 0.52 sec test 27 Start 27: SimdUnitTests 27: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/bin/simd-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/Testing/Temporary/SimdUnitTests.xml" 27: Test timeout computed to be: 30 27: [==========] Running 288 tests from 22 test cases. 27: [----------] Global test environment set-up. 27: [----------] 9 tests from SimdBootstrapTest 27: [ RUN ] SimdBootstrapTest.loadStore 27: [ OK ] SimdBootstrapTest.loadStore (0 ms) 27: [ RUN ] SimdBootstrapTest.loadU 27: [ OK ] SimdBootstrapTest.loadU (0 ms) 27: [ RUN ] SimdBootstrapTest.storeU 27: [ OK ] SimdBootstrapTest.storeU (0 ms) 27: [ RUN ] SimdBootstrapTest.loadStoreI 27: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) 27: [ RUN ] SimdBootstrapTest.loadUI 27: [ OK ] SimdBootstrapTest.loadUI (0 ms) 27: [ RUN ] SimdBootstrapTest.storeUI 27: [ OK ] SimdBootstrapTest.storeUI (0 ms) 27: [ RUN ] SimdBootstrapTest.simd4LoadStore 27: [ OK ] SimdBootstrapTest.simd4LoadStore (0 ms) 27: [ RUN ] SimdBootstrapTest.simd4LoadU 27: [ OK ] SimdBootstrapTest.simd4LoadU (0 ms) 27: [ RUN ] SimdBootstrapTest.simd4StoreU 27: [ OK ] SimdBootstrapTest.simd4StoreU (0 ms) 27: [----------] 9 tests from SimdBootstrapTest (0 ms total) 27: 27: [----------] 1 test from SimdTest 27: [ RUN ] SimdTest.GmxAligned 27: [ OK ] SimdTest.GmxAligned (0 ms) 27: [----------] 1 test from SimdTest (0 ms total) 27: 27: [----------] 42 tests from SimdFloatingpointTest 27: [ RUN ] SimdFloatingpointTest.setZero 27: [ OK ] SimdFloatingpointTest.setZero (0 ms) 27: [ RUN ] SimdFloatingpointTest.set 27: [ OK ] SimdFloatingpointTest.set (0 ms) 27: [ RUN ] SimdFloatingpointTest.add 27: [ OK ] SimdFloatingpointTest.add (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskAdd 27: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) 27: [ RUN ] SimdFloatingpointTest.sub 27: [ OK ] SimdFloatingpointTest.sub (0 ms) 27: [ RUN ] SimdFloatingpointTest.mul 27: [ OK ] SimdFloatingpointTest.mul (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskzMul 27: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) 27: [ RUN ] SimdFloatingpointTest.fma 27: [ OK ] SimdFloatingpointTest.fma (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskzFma 27: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) 27: [ RUN ] SimdFloatingpointTest.fms 27: [ OK ] SimdFloatingpointTest.fms (0 ms) 27: [ RUN ] SimdFloatingpointTest.fnma 27: [ OK ] SimdFloatingpointTest.fnma (0 ms) 27: [ RUN ] SimdFloatingpointTest.fnms 27: [ OK ] SimdFloatingpointTest.fnms (0 ms) 27: [ RUN ] SimdFloatingpointTest.abs 27: [ OK ] SimdFloatingpointTest.abs (0 ms) 27: [ RUN ] SimdFloatingpointTest.neg 27: [ OK ] SimdFloatingpointTest.neg (0 ms) 27: [ RUN ] SimdFloatingpointTest.and 27: [ OK ] SimdFloatingpointTest.and (0 ms) 27: [ RUN ] SimdFloatingpointTest.or 27: [ OK ] SimdFloatingpointTest.or (0 ms) 27: [ RUN ] SimdFloatingpointTest.xor 27: [ OK ] SimdFloatingpointTest.xor (0 ms) 27: [ RUN ] SimdFloatingpointTest.andNot 27: [ OK ] SimdFloatingpointTest.andNot (0 ms) 27: [ RUN ] SimdFloatingpointTest.max 27: [ OK ] SimdFloatingpointTest.max (0 ms) 27: [ RUN ] SimdFloatingpointTest.min 27: [ OK ] SimdFloatingpointTest.min (0 ms) 27: [ RUN ] SimdFloatingpointTest.round 27: [ OK ] SimdFloatingpointTest.round (0 ms) 27: [ RUN ] SimdFloatingpointTest.roundMode 27: [ OK ] SimdFloatingpointTest.roundMode (0 ms) 27: [ RUN ] SimdFloatingpointTest.trunc 27: [ OK ] SimdFloatingpointTest.trunc (0 ms) 27: [ RUN ] SimdFloatingpointTest.frexp 27: [ OK ] SimdFloatingpointTest.frexp (0 ms) 27: [ RUN ] SimdFloatingpointTest.ldexp 27: [ OK ] SimdFloatingpointTest.ldexp (0 ms) 27: [ RUN ] SimdFloatingpointTest.rsqrt 27: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskzRsqrt 27: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) 27: [ RUN ] SimdFloatingpointTest.rcp 27: [ OK ] SimdFloatingpointTest.rcp (0 ms) 27: [ RUN ] SimdFloatingpointTest.maskzRcp 27: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) 27: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask 27: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) 27: [ RUN ] SimdFloatingpointTest.selectByNotMask 27: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) 27: [ RUN ] SimdFloatingpointTest.cmpNe 27: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) 27: [ RUN ] SimdFloatingpointTest.cmpLe 27: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) 27: [ RUN ] SimdFloatingpointTest.cmpLt 27: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) 27: [ RUN ] SimdFloatingpointTest.testBits 27: [ OK ] SimdFloatingpointTest.testBits (0 ms) 27: [ RUN ] SimdFloatingpointTest.andB 27: [ OK ] SimdFloatingpointTest.andB (0 ms) 27: [ RUN ] SimdFloatingpointTest.orB 27: [ OK ] SimdFloatingpointTest.orB (0 ms) 27: [ RUN ] SimdFloatingpointTest.anyTrueB 27: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) 27: [ RUN ] SimdFloatingpointTest.blend 27: [ OK ] SimdFloatingpointTest.blend (0 ms) 27: [ RUN ] SimdFloatingpointTest.reduce 27: [ OK ] SimdFloatingpointTest.reduce (0 ms) 27: [ RUN ] SimdFloatingpointTest.cvtFloat2Double 27: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) 27: [ RUN ] SimdFloatingpointTest.cvtDouble2Float 27: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) 27: [----------] 42 tests from SimdFloatingpointTest (0 ms total) 27: 27: [----------] 16 tests from SimdFloatingpointUtilTest 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping 27: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets 27: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 27: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum 27: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.loadUNDuplicate4 27: [ OK ] SimdFloatingpointUtilTest.loadUNDuplicate4 (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.load4DuplicateN 27: [ OK ] SimdFloatingpointUtilTest.load4DuplicateN (0 ms) 27: [ RUN ] SimdFloatingpointUtilTest.loadU4NOffset 27: [ OK ] SimdFloatingpointUtilTest.loadU4NOffset (0 ms) 27: [----------] 16 tests from SimdFloatingpointUtilTest (0 ms total) 27: 27: [----------] 3 tests from SimdVectorOperationsTest 27: [ RUN ] SimdVectorOperationsTest.iprod 27: [ OK ] SimdVectorOperationsTest.iprod (0 ms) 27: [ RUN ] SimdVectorOperationsTest.norm2 27: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) 27: [ RUN ] SimdVectorOperationsTest.cprod 27: [ OK ] SimdVectorOperationsTest.cprod (0 ms) 27: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) 27: 27: [----------] 56 tests from SimdMathTest 27: [ RUN ] SimdMathTest.generateTestPointsFloat 27: [ OK ] SimdMathTest.generateTestPointsFloat (1 ms) 27: [ RUN ] SimdMathTest.copysign 27: [ OK ] SimdMathTest.copysign (0 ms) 27: [ RUN ] SimdMathTest.invsqrt 27: [ OK ] SimdMathTest.invsqrt (0 ms) 27: [ RUN ] SimdMathTest.maskzInvsqrt 27: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) 27: [ RUN ] SimdMathTest.invsqrtPair 27: [ OK ] SimdMathTest.invsqrtPair (1 ms) 27: [ RUN ] SimdMathTest.sqrt 27: [ OK ] SimdMathTest.sqrt (0 ms) 27: [ RUN ] SimdMathTest.sqrtUnsafe 27: [ OK ] SimdMathTest.sqrtUnsafe (0 ms) 27: [ RUN ] SimdMathTest.inv 27: [ OK ] SimdMathTest.inv (3 ms) 27: [ RUN ] SimdMathTest.maskzInv 27: [ OK ] SimdMathTest.maskzInv (0 ms) 27: [ RUN ] SimdMathTest.cbrt 27: [ OK ] SimdMathTest.cbrt (0 ms) 27: [ RUN ] SimdMathTest.invcbrt 27: [ OK ] SimdMathTest.invcbrt (2 ms) 27: [ RUN ] SimdMathTest.log2 27: [ OK ] SimdMathTest.log2 (0 ms) 27: [ RUN ] SimdMathTest.log 27: [ OK ] SimdMathTest.log (0 ms) 27: [ RUN ] SimdMathTest.exp2 27: [ OK ] SimdMathTest.exp2 (2 ms) 27: [ RUN ] SimdMathTest.exp2Unsafe 27: [ OK ] SimdMathTest.exp2Unsafe (0 ms) 27: [ RUN ] SimdMathTest.exp 27: [ OK ] SimdMathTest.exp (1 ms) 27: [ RUN ] SimdMathTest.expUnsafe 27: [ OK ] SimdMathTest.expUnsafe (1 ms) 27: [ RUN ] SimdMathTest.pow 27: [ OK ] SimdMathTest.pow (0 ms) 27: [ RUN ] SimdMathTest.powUnsafe 27: [ OK ] SimdMathTest.powUnsafe (0 ms) 27: [ RUN ] SimdMathTest.erf 27: [ OK ] SimdMathTest.erf (1 ms) 27: [ RUN ] SimdMathTest.erfc 27: [ OK ] SimdMathTest.erfc (0 ms) 27: [ RUN ] SimdMathTest.sin 27: [ OK ] SimdMathTest.sin (1 ms) 27: [ RUN ] SimdMathTest.cos 27: [ OK ] SimdMathTest.cos (1 ms) 27: [ RUN ] SimdMathTest.tan 27: [ OK ] SimdMathTest.tan (1 ms) 27: [ RUN ] SimdMathTest.asin 27: [ OK ] SimdMathTest.asin (0 ms) 27: [ RUN ] SimdMathTest.acos 27: [ OK ] SimdMathTest.acos (1 ms) 27: [ RUN ] SimdMathTest.atan 27: [ OK ] SimdMathTest.atan (0 ms) 27: [ RUN ] SimdMathTest.atan2 27: [ OK ] SimdMathTest.atan2 (0 ms) 27: [ RUN ] SimdMathTest.pmeForceCorrection 27: [ OK ] SimdMathTest.pmeForceCorrection (1 ms) 27: [ RUN ] SimdMathTest.pmePotentialCorrection 27: [ OK ] SimdMathTest.pmePotentialCorrection (1 ms) 27: [ RUN ] SimdMathTest.invsqrtSingleAccuracy 27: [ OK ] SimdMathTest.invsqrtSingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy 27: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.sqrtSingleAccuracy 27: [ OK ] SimdMathTest.sqrtSingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe 27: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (0 ms) 27: [ RUN ] SimdMathTest.invSingleAccuracy 27: [ OK ] SimdMathTest.invSingleAccuracy (2 ms) 27: [ RUN ] SimdMathTest.cbrtSingleAccuracy 27: [ OK ] SimdMathTest.cbrtSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.invcbrtSingleAccuracy 27: [ OK ] SimdMathTest.invcbrtSingleAccuracy (2 ms) 27: [ RUN ] SimdMathTest.log2SingleAccuracy 27: [ OK ] SimdMathTest.log2SingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.logSingleAccuracy 27: [ OK ] SimdMathTest.logSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.exp2SingleAccuracy 27: [ OK ] SimdMathTest.exp2SingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 27: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (1 ms) 27: [ RUN ] SimdMathTest.expSingleAccuracy 27: [ OK ] SimdMathTest.expSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe 27: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (0 ms) 27: [ RUN ] SimdMathTest.powSingleAccuracy 27: [ OK ] SimdMathTest.powSingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.powSingleAccuracyUnsafe 27: [ OK ] SimdMathTest.powSingleAccuracyUnsafe (0 ms) 27: [ RUN ] SimdMathTest.erfSingleAccuracy 27: [ OK ] SimdMathTest.erfSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.erfcSingleAccuracy 27: [ OK ] SimdMathTest.erfcSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.sinSingleAccuracy 27: [ OK ] SimdMathTest.sinSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.cosSingleAccuracy 27: [ OK ] SimdMathTest.cosSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.tanSingleAccuracy 27: [ OK ] SimdMathTest.tanSingleAccuracy (2 ms) 27: [ RUN ] SimdMathTest.asinSingleAccuracy 27: [ OK ] SimdMathTest.asinSingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.acosSingleAccuracy 27: [ OK ] SimdMathTest.acosSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.atanSingleAccuracy 27: [ OK ] SimdMathTest.atanSingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.atan2SingleAccuracy 27: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) 27: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy 27: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (1 ms) 27: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 27: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 27: [----------] 56 tests from SimdMathTest (37 ms total) 27: 27: [----------] 1 test from EmptyArrayRefTest 27: [ RUN ] EmptyArrayRefTest.IsEmpty 27: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 27: [----------] 1 test from EmptyArrayRefTest (0 ms total) 27: 27: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 27: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 27: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks 27: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) 27: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks 27: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) 27: [----------] 3 tests from ArrayRefTest/0 (0 ms total) 27: 27: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 27: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 27: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks 27: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) 27: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks 27: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) 27: [----------] 3 tests from ArrayRefTest/1 (0 ms total) 27: 27: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 27: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 27: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks 27: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) 27: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks 27: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) 27: [----------] 3 tests from ArrayRefTest/2 (0 ms total) 27: 27: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 27: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 27: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks 27: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) 27: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks 27: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) 27: [----------] 3 tests from ArrayRefTest/3 (0 ms total) 27: 27: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefReadWriteTest/0.Assignment 27: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) 27: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) 27: 27: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefReadWriteTest/1.Assignment 27: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) 27: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) 27: 27: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefArithmeticTest/0.Basic 27: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) 27: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) 27: 27: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef 27: [ RUN ] ArrayRefArithmeticTest/1.Basic 27: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) 27: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) 27: 27: [----------] 23 tests from SimdIntegerTest 27: [ RUN ] SimdIntegerTest.setZero 27: [ OK ] SimdIntegerTest.setZero (0 ms) 27: [ RUN ] SimdIntegerTest.set 27: [ OK ] SimdIntegerTest.set (0 ms) 27: [ RUN ] SimdIntegerTest.add 27: [ OK ] SimdIntegerTest.add (0 ms) 27: [ RUN ] SimdIntegerTest.sub 27: [ OK ] SimdIntegerTest.sub (0 ms) 27: [ RUN ] SimdIntegerTest.mul 27: [ OK ] SimdIntegerTest.mul (0 ms) 27: [ RUN ] SimdIntegerTest.and 27: [ OK ] SimdIntegerTest.and (0 ms) 27: [ RUN ] SimdIntegerTest.andNot 27: [ OK ] SimdIntegerTest.andNot (0 ms) 27: [ RUN ] SimdIntegerTest.or 27: [ OK ] SimdIntegerTest.or (0 ms) 27: [ RUN ] SimdIntegerTest.xor 27: [ OK ] SimdIntegerTest.xor (0 ms) 27: [ RUN ] SimdIntegerTest.extract 27: [ OK ] SimdIntegerTest.extract (0 ms) 27: [ RUN ] SimdIntegerTest.cvtR2I 27: [ OK ] SimdIntegerTest.cvtR2I (0 ms) 27: [ RUN ] SimdIntegerTest.cvttR2I 27: [ OK ] SimdIntegerTest.cvttR2I (0 ms) 27: [ RUN ] SimdIntegerTest.cvtI2R 27: [ OK ] SimdIntegerTest.cvtI2R (0 ms) 27: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask 27: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) 27: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask 27: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) 27: [ RUN ] SimdIntegerTest.cmpLt 27: [ OK ] SimdIntegerTest.cmpLt (0 ms) 27: [ RUN ] SimdIntegerTest.testBits 27: [ OK ] SimdIntegerTest.testBits (0 ms) 27: [ RUN ] SimdIntegerTest.andB 27: [ OK ] SimdIntegerTest.andB (0 ms) 27: [ RUN ] SimdIntegerTest.orB 27: [ OK ] SimdIntegerTest.orB (0 ms) 27: [ RUN ] SimdIntegerTest.anyTrue 27: [ OK ] SimdIntegerTest.anyTrue (0 ms) 27: [ RUN ] SimdIntegerTest.blend 27: [ OK ] SimdIntegerTest.blend (0 ms) 27: [ RUN ] SimdIntegerTest.cvtB2IB 27: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) 27: [ RUN ] SimdIntegerTest.cvtIB2B 27: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) 27: [----------] 23 tests from SimdIntegerTest (0 ms total) 27: 27: [----------] 32 tests from Simd4FloatingpointTest 27: [ RUN ] Simd4FloatingpointTest.setZero 27: [ OK ] Simd4FloatingpointTest.setZero (0 ms) 27: [ RUN ] Simd4FloatingpointTest.set 27: [ OK ] Simd4FloatingpointTest.set (0 ms) 27: [ RUN ] Simd4FloatingpointTest.add 27: [ OK ] Simd4FloatingpointTest.add (0 ms) 27: [ RUN ] Simd4FloatingpointTest.sub 27: [ OK ] Simd4FloatingpointTest.sub (0 ms) 27: [ RUN ] Simd4FloatingpointTest.mul 27: [ OK ] Simd4FloatingpointTest.mul (0 ms) 27: [ RUN ] Simd4FloatingpointTest.fma 27: [ OK ] Simd4FloatingpointTest.fma (0 ms) 27: [ RUN ] Simd4FloatingpointTest.fms 27: [ OK ] Simd4FloatingpointTest.fms (0 ms) 27: [ RUN ] Simd4FloatingpointTest.fnma 27: [ OK ] Simd4FloatingpointTest.fnma (0 ms) 27: [ RUN ] Simd4FloatingpointTest.fnms 27: [ OK ] Simd4FloatingpointTest.fnms (0 ms) 27: [ RUN ] Simd4FloatingpointTest.abs 27: [ OK ] Simd4FloatingpointTest.abs (0 ms) 27: [ RUN ] Simd4FloatingpointTest.neg 27: [ OK ] Simd4FloatingpointTest.neg (0 ms) 27: [ RUN ] Simd4FloatingpointTest.and 27: [ OK ] Simd4FloatingpointTest.and (0 ms) 27: [ RUN ] Simd4FloatingpointTest.or 27: [ OK ] Simd4FloatingpointTest.or (0 ms) 27: [ RUN ] Simd4FloatingpointTest.xor 27: [ OK ] Simd4FloatingpointTest.xor (0 ms) 27: [ RUN ] Simd4FloatingpointTest.andNot 27: [ OK ] Simd4FloatingpointTest.andNot (0 ms) 27: [ RUN ] Simd4FloatingpointTest.max 27: [ OK ] Simd4FloatingpointTest.max (0 ms) 27: [ RUN ] Simd4FloatingpointTest.min 27: [ OK ] Simd4FloatingpointTest.min (0 ms) 27: [ RUN ] Simd4FloatingpointTest.round 27: [ OK ] Simd4FloatingpointTest.round (0 ms) 27: [ RUN ] Simd4FloatingpointTest.trunc 27: [ OK ] Simd4FloatingpointTest.trunc (0 ms) 27: [ RUN ] Simd4FloatingpointTest.gmxSimd4RsqrtR 27: [ OK ] Simd4FloatingpointTest.gmxSimd4RsqrtR (0 ms) 27: [ RUN ] Simd4FloatingpointTest.cmpEqAndSelectByMask 27: [ OK ] Simd4FloatingpointTest.cmpEqAndSelectByMask (0 ms) 27: [ RUN ] Simd4FloatingpointTest.selectByNotMask 27: [ OK ] Simd4FloatingpointTest.selectByNotMask (0 ms) 27: [ RUN ] Simd4FloatingpointTest.cmpNe 27: [ OK ] Simd4FloatingpointTest.cmpNe (0 ms) 27: [ RUN ] Simd4FloatingpointTest.cmpLe 27: [ OK ] Simd4FloatingpointTest.cmpLe (0 ms) 27: [ RUN ] Simd4FloatingpointTest.cmpLt 27: [ OK ] Simd4FloatingpointTest.cmpLt (0 ms) 27: [ RUN ] Simd4FloatingpointTest.andB 27: [ OK ] Simd4FloatingpointTest.andB (0 ms) 27: [ RUN ] Simd4FloatingpointTest.orB 27: [ OK ] Simd4FloatingpointTest.orB (0 ms) 27: [ RUN ] Simd4FloatingpointTest.anyTrue 27: [ OK ] Simd4FloatingpointTest.anyTrue (0 ms) 27: [ RUN ] Simd4FloatingpointTest.blend 27: [ OK ] Simd4FloatingpointTest.blend (0 ms) 27: [ RUN ] Simd4FloatingpointTest.reduce 27: [ OK ] Simd4FloatingpointTest.reduce (0 ms) 27: [ RUN ] Simd4FloatingpointTest.dotProduct 27: [ OK ] Simd4FloatingpointTest.dotProduct (0 ms) 27: [ RUN ] Simd4FloatingpointTest.transpose 27: [ OK ] Simd4FloatingpointTest.transpose (0 ms) 27: [----------] 32 tests from Simd4FloatingpointTest (0 ms total) 27: 27: [----------] 1 test from Simd4VectorOperationsTest 27: [ RUN ] Simd4VectorOperationsTest.norm2 27: [ OK ] Simd4VectorOperationsTest.norm2 (0 ms) 27: [----------] 1 test from Simd4VectorOperationsTest (0 ms total) 27: 27: [----------] 2 tests from Simd4MathTest 27: [ RUN ] Simd4MathTest.invsqrt 27: [ OK ] Simd4MathTest.invsqrt (0 ms) 27: [ RUN ] Simd4MathTest.invsqrtSingleAccuracy 27: [ OK ] Simd4MathTest.invsqrtSingleAccuracy (0 ms) 27: [----------] 2 tests from Simd4MathTest (0 ms total) 27: 27: [----------] 41 tests from SimdScalarTest 27: [ RUN ] SimdScalarTest.load 27: [ OK ] SimdScalarTest.load (0 ms) 27: [ RUN ] SimdScalarTest.loadU 27: [ OK ] SimdScalarTest.loadU (0 ms) 27: [ RUN ] SimdScalarTest.store 27: [ OK ] SimdScalarTest.store (0 ms) 27: [ RUN ] SimdScalarTest.storeU 27: [ OK ] SimdScalarTest.storeU (0 ms) 27: [ RUN ] SimdScalarTest.setZero 27: [ OK ] SimdScalarTest.setZero (0 ms) 27: [ RUN ] SimdScalarTest.andNot 27: [ OK ] SimdScalarTest.andNot (0 ms) 27: [ RUN ] SimdScalarTest.fma 27: [ OK ] SimdScalarTest.fma (0 ms) 27: [ RUN ] SimdScalarTest.fms 27: [ OK ] SimdScalarTest.fms (0 ms) 27: [ RUN ] SimdScalarTest.fnma 27: [ OK ] SimdScalarTest.fnma (0 ms) 27: [ RUN ] SimdScalarTest.fnms 27: [ OK ] SimdScalarTest.fnms (0 ms) 27: [ RUN ] SimdScalarTest.maskAdd 27: [ OK ] SimdScalarTest.maskAdd (0 ms) 27: [ RUN ] SimdScalarTest.maskzMul 27: [ OK ] SimdScalarTest.maskzMul (0 ms) 27: [ RUN ] SimdScalarTest.maskzFma 27: [ OK ] SimdScalarTest.maskzFma (0 ms) 27: [ RUN ] SimdScalarTest.abs 27: [ OK ] SimdScalarTest.abs (0 ms) 27: [ RUN ] SimdScalarTest.max 27: [ OK ] SimdScalarTest.max (0 ms) 27: [ RUN ] SimdScalarTest.min 27: [ OK ] SimdScalarTest.min (0 ms) 27: [ RUN ] SimdScalarTest.round 27: [ OK ] SimdScalarTest.round (0 ms) 27: [ RUN ] SimdScalarTest.trunc 27: [ OK ] SimdScalarTest.trunc (0 ms) 27: [ RUN ] SimdScalarTest.reduce 27: [ OK ] SimdScalarTest.reduce (0 ms) 27: [ RUN ] SimdScalarTest.testBits 27: [ OK ] SimdScalarTest.testBits (0 ms) 27: [ RUN ] SimdScalarTest.anyTrue 27: [ OK ] SimdScalarTest.anyTrue (0 ms) 27: [ RUN ] SimdScalarTest.selectByMask 27: [ OK ] SimdScalarTest.selectByMask (0 ms) 27: [ RUN ] SimdScalarTest.selectByNotMask 27: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 27: [ RUN ] SimdScalarTest.blend 27: [ OK ] SimdScalarTest.blend (0 ms) 27: [ RUN ] SimdScalarTest.cvtR2I 27: [ OK ] SimdScalarTest.cvtR2I (0 ms) 27: [ RUN ] SimdScalarTest.cvttR2I 27: [ OK ] SimdScalarTest.cvttR2I (0 ms) 27: [ RUN ] SimdScalarTest.cvtI2R 27: [ OK ] SimdScalarTest.cvtI2R (0 ms) 27: [ RUN ] SimdScalarTest.cvtF2D 27: [ OK ] SimdScalarTest.cvtF2D (0 ms) 27: [ RUN ] SimdScalarTest.cvtD2D 27: [ OK ] SimdScalarTest.cvtD2D (0 ms) 27: [ RUN ] SimdScalarTest.loadI 27: [ OK ] SimdScalarTest.loadI (0 ms) 27: [ RUN ] SimdScalarTest.loadUI 27: [ OK ] SimdScalarTest.loadUI (0 ms) 27: [ RUN ] SimdScalarTest.storeI 27: [ OK ] SimdScalarTest.storeI (0 ms) 27: [ RUN ] SimdScalarTest.storeUI 27: [ OK ] SimdScalarTest.storeUI (0 ms) 27: [ RUN ] SimdScalarTest.andNotI 27: [ OK ] SimdScalarTest.andNotI (0 ms) 27: [ RUN ] SimdScalarTest.testBitsI 27: [ OK ] SimdScalarTest.testBitsI (0 ms) 27: [ RUN ] SimdScalarTest.selectByMaskI 27: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 27: [ RUN ] SimdScalarTest.selectByNotMaskI 27: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 27: [ RUN ] SimdScalarTest.blendI 27: [ OK ] SimdScalarTest.blendI (0 ms) 27: [ RUN ] SimdScalarTest.cvtB2IB 27: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 27: [ RUN ] SimdScalarTest.cvtIB2B 27: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 27: [ RUN ] SimdScalarTest.expandScalarsToTriplets 27: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 27: [----------] 41 tests from SimdScalarTest (0 ms total) 27: 27: [----------] 8 tests from SimdScalarUtilTest 27: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 27: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 27: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 27: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 27: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 27: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 27: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 27: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 27: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 27: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 27: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 27: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 27: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 27: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 27: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 27: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 27: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 27: 27: [----------] 37 tests from SimdScalarMathTest 27: [ RUN ] SimdScalarMathTest.copysign 27: [ OK ] SimdScalarMathTest.copysign (0 ms) 27: [ RUN ] SimdScalarMathTest.invsqrtPair 27: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 27: [ RUN ] SimdScalarMathTest.inv 27: [ OK ] SimdScalarMathTest.inv (0 ms) 27: [ RUN ] SimdScalarMathTest.maskzInvsqrt 27: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 27: [ RUN ] SimdScalarMathTest.log 27: [ OK ] SimdScalarMathTest.log (0 ms) 27: [ RUN ] SimdScalarMathTest.exp2 27: [ OK ] SimdScalarMathTest.exp2 (0 ms) 27: [ RUN ] SimdScalarMathTest.exp 27: [ OK ] SimdScalarMathTest.exp (0 ms) 27: [ RUN ] SimdScalarMathTest.erf 27: [ OK ] SimdScalarMathTest.erf (0 ms) 27: [ RUN ] SimdScalarMathTest.erfc 27: [ OK ] SimdScalarMathTest.erfc (0 ms) 27: [ RUN ] SimdScalarMathTest.sincos 27: [ OK ] SimdScalarMathTest.sincos (0 ms) 27: [ RUN ] SimdScalarMathTest.sin 27: [ OK ] SimdScalarMathTest.sin (0 ms) 27: [ RUN ] SimdScalarMathTest.cos 27: [ OK ] SimdScalarMathTest.cos (0 ms) 27: [ RUN ] SimdScalarMathTest.tan 27: [ OK ] SimdScalarMathTest.tan (0 ms) 27: [ RUN ] SimdScalarMathTest.asin 27: [ OK ] SimdScalarMathTest.asin (0 ms) 27: [ RUN ] SimdScalarMathTest.acos 27: [ OK ] SimdScalarMathTest.acos (0 ms) 27: [ RUN ] SimdScalarMathTest.atan 27: [ OK ] SimdScalarMathTest.atan (0 ms) 27: [ RUN ] SimdScalarMathTest.atan2 27: [ OK ] SimdScalarMathTest.atan2 (0 ms) 27: [ RUN ] SimdScalarMathTest.pmeForceCorrection 27: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 27: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 27: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 27: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 27: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.invSingleAccuracy 27: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 27: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.logSingleAccuracy 27: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 27: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.expSingleAccuracy 27: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 27: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 27: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 27: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 27: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 27: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 27: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 27: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 27: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 27: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 27: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 27: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 27: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 27: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 27: [----------] 37 tests from SimdScalarMathTest (0 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 288 tests from 22 test cases ran. (38 ms total) 27: [ PASSED ] 288 tests. 27/30 Test #27: SimdUnitTests .................... Passed 0.55 sec test 28 Start 28: CompatibilityHelpersTests 28: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/bin/compat-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/Testing/Temporary/CompatibilityHelpersTests.xml" 28: Test timeout computed to be: 30 28: [==========] Running 170 tests from 12 test cases. 28: [----------] Global test environment set-up. 28: [----------] 45 tests from OptionalTest 28: [ RUN ] OptionalTest.UnionCanContainNonPodTypes 28: [ OK ] OptionalTest.UnionCanContainNonPodTypes (0 ms) 28: [ RUN ] OptionalTest.CanDefaultConstructEmpty 28: [ OK ] OptionalTest.CanDefaultConstructEmpty (0 ms) 28: [ RUN ] OptionalTest.CanConstructFromNullopt 28: [ OK ] OptionalTest.CanConstructFromNullopt (0 ms) 28: [ RUN ] OptionalTest.CanDefaultConstructUsingNonDefaultConstructibleType 28: [ OK ] OptionalTest.CanDefaultConstructUsingNonDefaultConstructibleType (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptional 28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptional (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptional 28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptional (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptionalWithExplicitConversion 28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptionalWithExplicitConversion (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptionalNonExplicitConverting 28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptionalNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptionalExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptionalExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptionalNonExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptionalNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptional 28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptional (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptionalExplicitConverting 28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptionalExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptionalNonExplicitConverting 28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptionalNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptional 28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptional (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptionalExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptionalExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptionalNonExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptionalNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromLiteral 28: [ OK ] OptionalTest.CanCopyConstructFromLiteral (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromLiteralConverting 28: [ OK ] OptionalTest.CanCopyConstructFromLiteralConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromValue 28: [ OK ] OptionalTest.CanCopyConstructFromValue (0 ms) 28: [ RUN ] OptionalTest.CanCopyConstructFromValueConverting 28: [ OK ] OptionalTest.CanCopyConstructFromValueConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromValue 28: [ OK ] OptionalTest.CanMoveConstructFromValue (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromValueExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromValueExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveConstructFromValueNonExplicitConverting 28: [ OK ] OptionalTest.CanMoveConstructFromValueNonExplicitConverting (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceConstructFromLiteral 28: [ OK ] OptionalTest.CanInPlaceConstructFromLiteral (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceCopyConstructFromValue 28: [ OK ] OptionalTest.CanInPlaceCopyConstructFromValue (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceMoveConstructFromValue 28: [ OK ] OptionalTest.CanInPlaceMoveConstructFromValue (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceCopyConstructFromInitializerList 28: [ OK ] OptionalTest.CanInPlaceCopyConstructFromInitializerList (0 ms) 28: [ RUN ] OptionalTest.CanInPlaceMoveConstructFromInitializerList 28: [ OK ] OptionalTest.CanInPlaceMoveConstructFromInitializerList (0 ms) 28: [ RUN ] OptionalTest.CanAssignNulloptToDisengage 28: [ OK ] OptionalTest.CanAssignNulloptToDisengage (0 ms) 28: [ RUN ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionals 28: [ OK ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionals (0 ms) 28: [ RUN ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionalsConverting 28: [ OK ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionalsConverting (0 ms) 28: [ RUN ] OptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionalsConverting 28: [ OK ] OptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionalsConverting (0 ms) 28: [ RUN ] OptionalTest.CanCopyAssignFromLiteral 28: [ OK ] OptionalTest.CanCopyAssignFromLiteral (0 ms) 28: [ RUN ] OptionalTest.CanCopyAssignFromValue 28: [ OK ] OptionalTest.CanCopyAssignFromValue (0 ms) 28: [ RUN ] OptionalTest.CanMoveAssignFromValue 28: [ OK ] OptionalTest.CanMoveAssignFromValue (0 ms) 28: [ RUN ] OptionalTest.CanCopyEmplaceFromArguments 28: [ OK ] OptionalTest.CanCopyEmplaceFromArguments (0 ms) 28: [ RUN ] OptionalTest.CanMoveEmplaceFromArguments 28: [ OK ] OptionalTest.CanMoveEmplaceFromArguments (0 ms) 28: [ RUN ] OptionalTest.CanCopyEmplaceFromInitializerListAndArguments 28: [ OK ] OptionalTest.CanCopyEmplaceFromInitializerListAndArguments (0 ms) 28: [ RUN ] OptionalTest.CanMoveEmplaceFromInitializerListAndArguments 28: [ OK ] OptionalTest.CanMoveEmplaceFromInitializerListAndArguments (0 ms) 28: [ RUN ] OptionalTest.CanResetContent 28: [ OK ] OptionalTest.CanResetContent (0 ms) 28: [ RUN ] OptionalTest.ProvidesRelationalOperators 28: [ OK ] OptionalTest.ProvidesRelationalOperators (0 ms) 28: [ RUN ] OptionalTest.ProvidesMixedTypeRelationalOperators 28: [ OK ] OptionalTest.ProvidesMixedTypeRelationalOperators (0 ms) 28: [ RUN ] OptionalTest.CanProduceHash 28: [ OK ] OptionalTest.CanProduceHash (0 ms) 28: [ RUN ] OptionalTest.ShowAlignmentDependingOnBaseType 28: alignment_of: 1 28: alignment_of: 2 28: alignment_of: 4 28: alignment_of: 8 28: alignment_of: 4 28: alignment_of: 8 28: alignment_of: 16 28: alignment_of: 1 28: [ OK ] OptionalTest.ShowAlignmentDependingOnBaseType (0 ms) 28: [ RUN ] OptionalTest.ShowSizeDependingOnBaseType 28: sizeof( nonstd::optional_lite::detail::storage_t ): 1 28: sizeof( optional ): 2 (1) 28: sizeof( optional ): 4 (2) 28: sizeof( optional ): 8 (4) 28: sizeof( optional ): 16 (8) 28: sizeof( optional ): 8 (4) 28: sizeof( optional ): 16 (8) 28: sizeof( optional ): 32 (16) 28: sizeof( optional ): 2 (1) 28: [ OK ] OptionalTest.ShowSizeDependingOnBaseType (0 ms) 28: [----------] 45 tests from OptionalTest (1 ms total) 28: 28: [----------] 7 tests from MakeOptionalTest 28: [ RUN ] MakeOptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionals 28: [ OK ] MakeOptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionals (0 ms) 28: [ RUN ] MakeOptionalTest.CanCopyConstruct 28: [ OK ] MakeOptionalTest.CanCopyConstruct (0 ms) 28: [ RUN ] MakeOptionalTest.CanMoveConstruct 28: [ OK ] MakeOptionalTest.CanMoveConstruct (0 ms) 28: [ RUN ] MakeOptionalTest.CanInPlaceCopyConstructFromArguments 28: [ OK ] MakeOptionalTest.CanInPlaceCopyConstructFromArguments (0 ms) 28: [ RUN ] MakeOptionalTest.CanInPlaceMoveConstructFromArguments 28: [ OK ] MakeOptionalTest.CanInPlaceMoveConstructFromArguments (0 ms) 28: [ RUN ] MakeOptionalTest.CanInPlaceCopyConstructFromInitializerListAndArguments 28: [ OK ] MakeOptionalTest.CanInPlaceCopyConstructFromInitializerListAndArguments (0 ms) 28: [ RUN ] MakeOptionalTest.CanInPlaceMoveConstructFromInitializerListAndArguments 28: [ OK ] MakeOptionalTest.CanInPlaceMoveConstructFromInitializerListAndArguments (0 ms) 28: [----------] 7 tests from MakeOptionalTest (0 ms total) 28: 28: [----------] 4 tests from OptionalMemberSwapTest 28: [ RUN ] OptionalMemberSwapTest.CanSwapDisengagedWithDisengaged 28: [ OK ] OptionalMemberSwapTest.CanSwapDisengagedWithDisengaged (0 ms) 28: [ RUN ] OptionalMemberSwapTest.CanSwapEngagedWithDisengaged 28: [ OK ] OptionalMemberSwapTest.CanSwapEngagedWithDisengaged (0 ms) 28: [ RUN ] OptionalMemberSwapTest.CanSwapDisengagedWithEngaged 28: [ OK ] OptionalMemberSwapTest.CanSwapDisengagedWithEngaged (0 ms) 28: [ RUN ] OptionalMemberSwapTest.CanSwapEngagedWithEngaged 28: [ OK ] OptionalMemberSwapTest.CanSwapEngagedWithEngaged (0 ms) 28: [----------] 4 tests from OptionalMemberSwapTest (0 ms total) 28: 28: [----------] 4 tests from OptionalImplicitValueTest 28: [ RUN ] OptionalImplicitValueTest.CanObtainValueConst 28: [ OK ] OptionalImplicitValueTest.CanObtainValueConst (0 ms) 28: [ RUN ] OptionalImplicitValueTest.CanObtainValueNonConst 28: [ OK ] OptionalImplicitValueTest.CanObtainValueNonConst (0 ms) 28: [ RUN ] OptionalImplicitValueTest.CanObtainMovedFromValueConst 28: [ OK ] OptionalImplicitValueTest.CanObtainMovedFromValueConst (0 ms) 28: [ RUN ] OptionalImplicitValueTest.CanObtainMovedFromValueNonConst 28: [ OK ] OptionalImplicitValueTest.CanObtainMovedFromValueNonConst (0 ms) 28: [----------] 4 tests from OptionalImplicitValueTest (0 ms total) 28: 28: [----------] 20 tests from OptionalIntValueTest 28: [ RUN ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorConst 28: [ OK ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorNonConst 28: [ OK ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorNonConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorConst 28: [ OK ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorNonConst 28: [ OK ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorNonConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainHasValueViaOperatorBool 28: [ OK ] OptionalIntValueTest.CanObtainHasValueViaOperatorBool (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainValueViaValueMethodConst 28: [ OK ] OptionalIntValueTest.CanObtainValueViaValueMethodConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainValueViaValueMethodNonConst 28: [ OK ] OptionalIntValueTest.CanObtainValueViaValueMethodNonConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodConst 28: [ OK ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodNonConst 28: [ OK ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodNonConst (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainValueFromNonEmptyOptionalViaValueOrMethod 28: [ OK ] OptionalIntValueTest.CanObtainValueFromNonEmptyOptionalViaValueOrMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainDefaultFromEmptyOptionalViaValueOrMethod 28: [ OK ] OptionalIntValueTest.CanObtainDefaultFromEmptyOptionalViaValueOrMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedFromValueForLValuesViaValueOrMethod 28: [ OK ] OptionalIntValueTest.CanObtainMovedFromValueForLValuesViaValueOrMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.CanObtainMovedFromValueForRValuesViaValueOrMethod 28: [ OK ] OptionalIntValueTest.CanObtainMovedFromValueForRValuesViaValueOrMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForLValues 28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForLValues (0 ms) 28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForRValues 28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForRValues (0 ms) 28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessWithNonEmptyWhatMethod 28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessWithNonEmptyWhatMethod (0 ms) 28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithDisengaged 28: [ OK ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithDisengaged (0 ms) 28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithEngaged 28: [ OK ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithEngaged (0 ms) 28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithEngaged 28: [ OK ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithEngaged (0 ms) 28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithDisengaged 28: [ OK ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithDisengaged (0 ms) 28: [----------] 20 tests from OptionalIntValueTest (0 ms total) 28: 28: [----------] 1 test from NotNullConstruction 28: [ RUN ] NotNullConstruction.Works 28: [ OK ] NotNullConstruction.Works (0 ms) 28: [----------] 1 test from NotNullConstruction (0 ms total) 28: 28: [----------] 1 test from NotNullCasting 28: [ RUN ] NotNullCasting.Works 28: [ OK ] NotNullCasting.Works (0 ms) 28: [----------] 1 test from NotNullCasting (0 ms total) 28: 28: [----------] 1 test from NotNullAssignment 28: [ RUN ] NotNullAssignment.Works 28: [ OK ] NotNullAssignment.Works (0 ms) 28: [----------] 1 test from NotNullAssignment (0 ms total) 28: 28: [----------] 1 test from MakeNotNull 28: [ RUN ] MakeNotNull.Works 28: [ OK ] MakeNotNull.Works (0 ms) 28: [----------] 1 test from MakeNotNull (0 ms total) 28: 28: [----------] 1 test from NotNull 28: [ RUN ] NotNull.WorksInContainers 28: [ OK ] NotNull.WorksInContainers (0 ms) 28: [----------] 1 test from NotNull (0 ms total) 28: 28: [----------] 80 tests from StringViewTest 28: [ RUN ] StringViewTest.CanDefaultConstructEmptyView 28: [ OK ] StringViewTest.CanDefaultConstructEmptyView (0 ms) 28: [ RUN ] StringViewTest.CanConstructFromPointerAndSize 28: [ OK ] StringViewTest.CanConstructFromPointerAndSize (0 ms) 28: [ RUN ] StringViewTest.CanConstructFromCString 28: [ OK ] StringViewTest.CanConstructFromCString (0 ms) 28: [ RUN ] StringViewTest.CanCopyConstructFromEmptyView 28: [ OK ] StringViewTest.CanCopyConstructFromEmptyView (0 ms) 28: [ RUN ] StringViewTest.CanCopyConstructFromNonEmptyView 28: [ OK ] StringViewTest.CanCopyConstructFromNonEmptyView (0 ms) 28: [ RUN ] StringViewTest.CanCopyAssingFromEmptyView 28: [ OK ] StringViewTest.CanCopyAssingFromEmptyView (0 ms) 28: [ RUN ] StringViewTest.CanCopyAssingFromNonEmptyView 28: [ OK ] StringViewTest.CanCopyAssingFromNonEmptyView (0 ms) 28: [ RUN ] StringViewTest.AllowForwardIteration 28: [ OK ] StringViewTest.AllowForwardIteration (0 ms) 28: [ RUN ] StringViewTest.AllowConstForwardIteration 28: [ OK ] StringViewTest.AllowConstForwardIteration (0 ms) 28: [ RUN ] StringViewTest.AllowReverseIteration 28: [ OK ] StringViewTest.AllowReverseIteration (0 ms) 28: [ RUN ] StringViewTest.AllowConstReverseIteration 28: [ OK ] StringViewTest.AllowConstReverseIteration (0 ms) 28: [ RUN ] StringViewTest.CanObtainSizeFromViewViaSize 28: [ OK ] StringViewTest.CanObtainSizeFromViewViaSize (0 ms) 28: [ RUN ] StringViewTest.CanObtainSizeFromViewViaLength 28: [ OK ] StringViewTest.CanObtainSizeFromViewViaLength (0 ms) 28: [ RUN ] StringViewTest.CanObtainMaxSizeViaMaxSize 28: [ OK ] StringViewTest.CanObtainMaxSizeViaMaxSize (0 ms) 28: [ RUN ] StringViewTest.CanCheckForEmptyStringWithEmpty 28: [ OK ] StringViewTest.CanCheckForEmptyStringWithEmpty (0 ms) 28: [ RUN ] StringViewTest.CanAccessElementViaArrayIndex 28: [ OK ] StringViewTest.CanAccessElementViaArrayIndex (0 ms) 28: [ RUN ] StringViewTest.CanAccessElementViaAt 28: [ OK ] StringViewTest.CanAccessElementViaAt (0 ms) 28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsAccess 28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsAccess (0 ms) 28: [ RUN ] StringViewTest.CanAccessAllElementsViaData 28: [ OK ] StringViewTest.CanAccessAllElementsViaData (0 ms) 28: [ RUN ] StringViewTest.DataFromEmptyStringIsNullptr 28: [ OK ] StringViewTest.DataFromEmptyStringIsNullptr (0 ms) 28: [ RUN ] StringViewTest.CanRemovePrefix 28: [ OK ] StringViewTest.CanRemovePrefix (0 ms) 28: [ RUN ] StringViewTest.CanRemoveSuffix 28: [ OK ] StringViewTest.CanRemoveSuffix (0 ms) 28: [ RUN ] StringViewTest.CanSwapWithOtherView 28: [ OK ] StringViewTest.CanSwapWithOtherView (0 ms) 28: [ RUN ] StringViewTest.CanCopySubstringWithCopy 28: [ OK ] StringViewTest.CanCopySubstringWithCopy (0 ms) 28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsCopy 28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsCopy (0 ms) 28: [ RUN ] StringViewTest.CanObtainSubstringWithSubstr 28: [ OK ] StringViewTest.CanObtainSubstringWithSubstr (0 ms) 28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsSubstr 28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsSubstr (0 ms) 28: [ RUN ] StringViewTest.CanLexicallyCompareViewWithCompare 28: [ OK ] StringViewTest.CanLexicallyCompareViewWithCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareEmptyViewsWIthCompare 28: [ OK ] StringViewTest.CanCompareEmptyViewsWIthCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareSubStringWithViewViaCompare 28: [ OK ] StringViewTest.CanCompareSubStringWithViewViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareSubStringWithSubStringViewViaCompare 28: [ OK ] StringViewTest.CanCompareSubStringWithSubStringViewViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareToCStringViaCompare 28: [ OK ] StringViewTest.CanCompareToCStringViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareSubStringToCStringViaCompare 28: [ OK ] StringViewTest.CanCompareSubStringToCStringViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCompareSubStringToCStringPrefixViaCompare 28: [ OK ] StringViewTest.CanCompareSubStringToCStringPrefixViaCompare (0 ms) 28: [ RUN ] StringViewTest.CanCheckForPrefixViewViaStartsWith 28: [ OK ] StringViewTest.CanCheckForPrefixViewViaStartsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForPrefixCharacterViaStartsWith 28: [ OK ] StringViewTest.CanCheckForPrefixCharacterViaStartsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForPrefixCStringViaStartsWith 28: [ OK ] StringViewTest.CanCheckForPrefixCStringViaStartsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForSuffixViewViaEndsWith 28: [ OK ] StringViewTest.CanCheckForSuffixViewViaEndsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForSuffixCharacterViaEndsWith 28: [ OK ] StringViewTest.CanCheckForSuffixCharacterViaEndsWith (0 ms) 28: [ RUN ] StringViewTest.CanCheckForSuffixCStringViaEndsWith 28: [ OK ] StringViewTest.CanCheckForSuffixCStringViaEndsWith (0 ms) 28: [ RUN ] StringViewTest.CanSearchForViewSubstrViaFind 28: [ OK ] StringViewTest.CanSearchForViewSubstrViaFind (0 ms) 28: [ RUN ] StringViewTest.CanSearchForCharacterViaFind 28: [ OK ] StringViewTest.CanSearchForCharacterViaFind (0 ms) 28: [ RUN ] StringViewTest.CanSearchForCStringSubstringViaFind 28: [ OK ] StringViewTest.CanSearchForCStringSubstringViaFind (0 ms) 28: [ RUN ] StringViewTest.CanSearchForCStringSubstringViaFindWithDefaultPos 28: [ OK ] StringViewTest.CanSearchForCStringSubstringViaFindWithDefaultPos (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForViewSubstrViaFind 28: [ OK ] StringViewTest.CanBackwardsSearchForViewSubstrViaFind (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForCharacterViaFind 28: [ OK ] StringViewTest.CanBackwardsSearchForCharacterViaFind (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFind 28: [ OK ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFind (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFindWithDefaultPos 28: [ OK ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFindWithDefaultPos (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfAnyCharacterInView 28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfAnyCharacterInView (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharacter 28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharacter (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCStringInLenght 28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCStringInLenght (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCString 28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCString (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfAnyCharacterInView 28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfAnyCharacterInView (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharacter 28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharacter (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCStringInLenght 28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCStringInLenght (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCString 28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCString (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstNotFoundCharacter 28: [ OK ] StringViewTest.CanSearchForFirstNotFoundCharacter (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstNonMatchingCharacter 28: [ OK ] StringViewTest.CanSearchForFirstNonMatchingCharacter (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCStringInLength 28: [ OK ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCStringInLength (0 ms) 28: [ RUN ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCString 28: [ OK ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCString (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForForstNonFoundCharacterInView 28: [ OK ] StringViewTest.CanBackwardsSearchForForstNonFoundCharacterInView (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonMatchingCharacter 28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonMatchingCharacter (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCStringInLength 28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCStringInLength (0 ms) 28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCString 28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCString (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSV 28: [ OK ] StringViewTest.CanCreateViewWithLiteralSV (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsStringViewLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsStringViewLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInStringViewLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInStringViewLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SV 28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SV (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsStringViewLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsStringViewLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInStringViewLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInStringViewLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsNamespace 28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsNamespace (0 ms) 28: [ RUN ] StringViewTest.CanCompareToViews 28: [ OK ] StringViewTest.CanCompareToViews (0 ms) 28: [ RUN ] StringViewTest.CanCompareViewToImplicitlyConvertedView 28: [ OK ] StringViewTest.CanCompareViewToImplicitlyConvertedView (0 ms) 28: [ RUN ] StringViewTest.EmptyViewsCompareAsEqual 28: [ OK ] StringViewTest.EmptyViewsCompareAsEqual (0 ms) 28: [ RUN ] StringViewTest.CanPrintViewToPutputStream 28: [ OK ] StringViewTest.CanPrintViewToPutputStream (0 ms) 28: [ RUN ] StringViewTest.HashOfViewIsEqualToHashOfString 28: [ OK ] StringViewTest.HashOfViewIsEqualToHashOfString (0 ms) 28: [ RUN ] StringViewTest.HashOfWStringViewIsEqualToHashOfString 28: [ OK ] StringViewTest.HashOfWStringViewIsEqualToHashOfString (0 ms) 28: [ RUN ] StringViewTest.HashOfU16StringViewIsEqualToHashOfString 28: [ OK ] StringViewTest.HashOfU16StringViewIsEqualToHashOfString (0 ms) 28: [ RUN ] StringViewTest.HashOfU32StringViewIsEqualToHashOfString 28: [ OK ] StringViewTest.HashOfU32StringViewIsEqualToHashOfString (0 ms) 28: [----------] 80 tests from StringViewTest (1 ms total) 28: 28: [----------] 5 tests from StringViewExtensionTest 28: [ RUN ] StringViewExtensionTest.CanConstructViewFromString 28: [ OK ] StringViewExtensionTest.CanConstructViewFromString (0 ms) 28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaExplicitOperator 28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaExplicitOperator (0 ms) 28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaToString 28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaToString (0 ms) 28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaToStringFreeFunction 28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaToStringFreeFunction (0 ms) 28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViewViaToStringView 28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViewViaToStringView (0 ms) 28: [----------] 5 tests from StringViewExtensionTest (0 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 170 tests from 12 test cases ran. (2 ms total) 28: [ PASSED ] 170 tests. 28/30 Test #28: CompatibilityHelpersTests ........ Passed 0.50 sec test 29 Start 29: FileIOTests 29: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/bin/fileio-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/Testing/Temporary/FileIOTests.xml" 29: Test timeout computed to be: 30 29: [==========] Running 33 tests from 8 test cases. 29: [----------] Global test environment set-up. 29: [----------] 2 tests from FileMD5Test 29: [ RUN ] FileMD5Test.CanComputeMD5 29: [ OK ] FileMD5Test.CanComputeMD5 (1 ms) 29: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 29: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 29: [----------] 2 tests from FileMD5Test (1 ms total) 29: 29: [----------] 3 tests from MrcSerializer 29: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet 29: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) 29: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize 29: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (1 ms) 29: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip 29: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (0 ms) 29: [----------] 3 tests from MrcSerializer (2 ms total) 29: 29: [----------] 4 tests from MrcDensityMap 29: [ RUN ] MrcDensityMap.RoundTripIsIdempotent 29: [ OK ] MrcDensityMap.RoundTripIsIdempotent (0 ms) 29: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent 29: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (1 ms) 29: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile 29: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms) 29: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile 29: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (1 ms) 29: [----------] 4 tests from MrcDensityMap (3 ms total) 29: 29: [----------] 8 tests from MrcDensityMapHeaderTest 29: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader 29: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) 29: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect 29: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) 29: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid 29: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms) 29: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven 29: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) 29: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined 29: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms) 29: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues 29: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) 29: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents 29: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) 29: [ RUN ] MrcDensityMapHeaderTest.IsSane 29: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) 29: [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total) 29: 29: [----------] 9 tests from ReadTest 29: [ RUN ] ReadTest.get_eint_ReadsInteger 29: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 29: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 29: 29: ERROR 1 [file unknown, line 0]: 29: Right hand side '0.8' for parameter 'test' in parameter file is not an 29: integer value 29: 29: 29: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 29: [ RUN ] ReadTest.get_eint_WarnsAboutString 29: 29: ERROR 1 [file unknown, line 0]: 29: Right hand side 'hello' for parameter 'test' in parameter file is not an 29: integer value 29: 29: 29: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 29: [ RUN ] ReadTest.get_eint64_ReadsInteger 29: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 29: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 29: 29: ERROR 1 [file unknown, line 0]: 29: Right hand side '0.8' for parameter 'test' in parameter file is not an 29: integer value 29: 29: 29: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 29: [ RUN ] ReadTest.get_eint64_WarnsAboutString 29: 29: ERROR 1 [file unknown, line 0]: 29: Right hand side 'hello' for parameter 'test' in parameter file is not an 29: integer value 29: 29: 29: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 29: [ RUN ] ReadTest.get_ereal_ReadsInteger 29: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 29: [ RUN ] ReadTest.get_ereal_ReadsFloat 29: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 29: [ RUN ] ReadTest.get_ereal_WarnsAboutString 29: 29: ERROR 1 [file unknown, line 0]: 29: Right hand side 'hello' for parameter 'test' in parameter file is not a 29: real value 29: 29: 29: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 29: [----------] 9 tests from ReadTest (0 ms total) 29: 29: [----------] 1 test from FileIOXdrSerializerTest 29: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect 29: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (0 ms) 29: [----------] 1 test from FileIOXdrSerializerTest (0 ms total) 29: 29: [----------] 2 tests from TngTest 29: [ RUN ] TngTest.CanOpenTngFile 29: TNG library: Cannot open file spc2-traj.tng. ./src/external/tng_io/src/lib/tng_io.c: 890 29: TNG library: Cannot open file spc2-traj.tng. ./src/external/tng_io/src/lib/tng_io.c: 890 29: [ OK ] TngTest.CanOpenTngFile (0 ms) 29: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 29: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 29: [----------] 2 tests from TngTest (0 ms total) 29: 29: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 29: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 29: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (1 ms) 29: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 29: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (1 ms) 29: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 29: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (10 ms) 29: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 29: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (1 ms) 29: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (13 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 33 tests from 8 test cases ran. (19 ms total) 29: [ PASSED ] 33 tests. 29/30 Test #29: FileIOTests ...................... Passed 0.48 sec test 30 Start 30: SelectionUnitTests 30: Test command: /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/bin/selection-test "--gtest_output=xml:/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/Testing/Temporary/SelectionUnitTests.xml" 30: Test timeout computed to be: 30 30: [==========] Running 192 tests from 11 test cases. 30: [----------] Global test environment set-up. 30: [----------] 1 test from IndexGroupTest 30: [ RUN ] IndexGroupTest.RemovesDuplicates 30: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 30: [----------] 1 test from IndexGroupTest (0 ms total) 30: 30: [----------] 15 tests from IndexBlockTest 30: [ RUN ] IndexBlockTest.CreatesUnknownBlock 30: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms) 30: [ RUN ] IndexBlockTest.CreatesAtomBlock 30: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms) 30: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology 30: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms) 30: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology 30: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (1 ms) 30: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology 30: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms) 30: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology 30: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms) 30: [ RUN ] IndexBlockTest.CreatesSingleBlock 30: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) 30: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 30: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (136 ms) 30: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 30: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) 30: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 30: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 30: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 30: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (11 ms) 30: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 30: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 30: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 30: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 30: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 30: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 30: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 30: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 30: [----------] 15 tests from IndexBlockTest (149 ms total) 30: 30: [----------] 11 tests from IndexMapTest 30: [ RUN ] IndexMapTest.InitializesAtomBlock 30: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms) 30: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 30: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms) 30: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 30: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms) 30: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 30: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) 30: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 30: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms) 30: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 30: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms) 30: [ RUN ] IndexMapTest.InitializesMoleculeBlock 30: [ OK ] IndexMapTest.InitializesMoleculeBlock (1 ms) 30: [ RUN ] IndexMapTest.MapsSingleBlock 30: [ OK ] IndexMapTest.MapsSingleBlock (0 ms) 30: [ RUN ] IndexMapTest.MapsResidueBlocks 30: [ OK ] IndexMapTest.MapsResidueBlocks (0 ms) 30: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 30: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms) 30: [ RUN ] IndexMapTest.HandlesMultipleRequests 30: [ OK ] IndexMapTest.HandlesMultipleRequests (1 ms) 30: [----------] 11 tests from IndexMapTest (2 ms total) 30: 30: [----------] 3 tests from IndexGroupsAndNamesTest 30: [ RUN ] IndexGroupsAndNamesTest.containsNames 30: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms) 30: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing 30: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms) 30: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect 30: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms) 30: [----------] 3 tests from IndexGroupsAndNamesTest (0 ms total) 30: 30: [----------] 15 tests from NeighborhoodSearchTest 30: [ RUN ] NeighborhoodSearchTest.SimpleSearch 30: [ OK ] NeighborhoodSearchTest.SimpleSearch (11 ms) 30: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 30: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (11 ms) 30: [ RUN ] NeighborhoodSearchTest.GridSearchBox 30: [ OK ] NeighborhoodSearchTest.GridSearchBox (2 ms) 30: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 30: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (6 ms) 30: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 30: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (3 ms) 30: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 30: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (1 ms) 30: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 30: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (2 ms) 30: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 30: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 30: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 30: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (40 ms) 30: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 30: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) 30: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 30: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 30: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 30: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 30: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 30: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 30: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 30: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (12 ms) 30: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 30: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (1 ms) 30: [----------] 15 tests from NeighborhoodSearchTest (89 ms total) 30: 30: [----------] 12 tests from PositionCalculationTest 30: [ RUN ] PositionCalculationTest.ComputesAtomPositions 30: [ OK ] PositionCalculationTest.ComputesAtomPositions (0 ms) 30: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 30: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (1 ms) 30: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 30: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (0 ms) 30: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 30: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms) 30: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 30: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms) 30: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 30: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms) 30: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 30: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (1 ms) 30: [ RUN ] PositionCalculationTest.ComputesPositionMask 30: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms) 30: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 30: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms) 30: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 30: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms) 30: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 30: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (0 ms) 30: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 30: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (1 ms) 30: [----------] 12 tests from PositionCalculationTest (3 ms total) 30: 30: [----------] 29 tests from SelectionCollectionTest 30: [ RUN ] SelectionCollectionTest.HandlesNoSelections 30: [ OK ] SelectionCollectionTest.HandlesNoSelections (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 30: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 30: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 30: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (1 ms) 30: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 30: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 30: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 30: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (1 ms) 30: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 30: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 30: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 30: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (1 ms) 30: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 30: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 30: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 30: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (1 ms) 30: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 30: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 30: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 30: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (1 ms) 30: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 30: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 30: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 30: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (1 ms) 30: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 30: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (0 ms) 30: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 30: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (0 ms) 30: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 30: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (0 ms) 30: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 30: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (1 ms) 30: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 30: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (0 ms) 30: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 30: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 30: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 30: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (1 ms) 30: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 30: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (0 ms) 30: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 30: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (0 ms) 30: [----------] 29 tests from SelectionCollectionTest (8 ms total) 30: 30: [----------] 14 tests from SelectionCollectionInteractiveTest 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 30: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (1 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 30: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (0 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 30: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (1 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 30: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (0 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 30: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (0 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 30: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (1 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 30: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (0 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 30: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (0 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 30: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (1 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 30: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (0 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 30: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (0 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 30: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (1 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 30: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (0 ms) 30: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 30: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (0 ms) 30: [----------] 14 tests from SelectionCollectionInteractiveTest (5 ms total) 30: 30: [----------] 66 tests from SelectionCollectionDataTest 30: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 30: [ OK ] SelectionCollectionDataTest.HandlesAllNone (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 30: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesResnr 30: [ OK ] SelectionCollectionDataTest.HandlesResnr (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 30: [ OK ] SelectionCollectionDataTest.HandlesResIndex (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 30: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 30: [ OK ] SelectionCollectionDataTest.HandlesAtomname (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 30: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 30: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesChain 30: [ OK ] SelectionCollectionDataTest.HandlesChain (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesMass 30: [ OK ] SelectionCollectionDataTest.HandlesMass (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesCharge 30: [ OK ] SelectionCollectionDataTest.HandlesCharge (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 30: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 30: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 30: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesBeta 30: [ OK ] SelectionCollectionDataTest.HandlesBeta (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesResname 30: [ OK ] SelectionCollectionDataTest.HandlesResname (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 30: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 30: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 30: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 30: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (2 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 30: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 30: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 30: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 30: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (4 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 30: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 30: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 30: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (1 ms) 30: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 30: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (1 ms) 30: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 30: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 30: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 30: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 30: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 30: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 30: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 30: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 30: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 30: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 30: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 30: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 30: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 30: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 30: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 30: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 30: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 30: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 30: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 30: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 30: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 30: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 30: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 30: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 30: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 30: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 30: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 30: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 30: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 30: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 30: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 30: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 30: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 30: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 30: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 30: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (1 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 30: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 30: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (0 ms) 30: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 30: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (1 ms) 30: [----------] 66 tests from SelectionCollectionDataTest (48 ms total) 30: 30: [----------] 17 tests from SelectionOptionTest 30: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 30: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 30: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 30: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (1 ms) 30: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 30: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (0 ms) 30: [ RUN ] SelectionOptionTest.ChecksEmptySelections 30: [ OK ] SelectionOptionTest.ChecksEmptySelections (0 ms) 30: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 30: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesTooManySelections 30: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 30: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 30: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (1 ms) 30: [ RUN ] SelectionOptionTest.HandlesAdjuster 30: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 30: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 30: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 30: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 30: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 30: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms) 30: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 30: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (1 ms) 30: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 30: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms) 30: [----------] 17 tests from SelectionOptionTest (3 ms total) 30: 30: [----------] 9 tests from SelectionFileOptionTest 30: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 30: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (0 ms) 30: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 30: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (0 ms) 30: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 30: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) 30: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 30: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (0 ms) 30: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 30: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (1 ms) 30: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 30: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (0 ms) 30: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 30: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms) 30: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 30: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (29 ms) 30: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 30: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (0 ms) 30: [----------] 9 tests from SelectionFileOptionTest (30 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 192 tests from 11 test cases ran. (338 ms total) 30: [ PASSED ] 192 tests. 30/30 Test #30: SelectionUnitTests ............... Passed 1.00 sec 100% tests passed, 0 tests failed out of 30 Label Time Summary: GTest = 19.57 sec*proc (30 tests) MpiTest = 2.08 sec*proc (3 tests) UnitTest = 19.57 sec*proc (30 tests) Total Test time (real) = 20.31 sec touch build-openmpi dh_testdir dh_testroot dh_prep -pgromacs dh_installdirs -pgromacs /usr/bin/make -j4 -C build/basic install DESTDIR=/build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs make[1]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/cmake -S/build/gromacs-5atmZb/gromacs-2020.6 -B/build/gromacs-5atmZb/gromacs-2020.6/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-5atmZb/gromacs-2020.6/build/basic/CMakeFiles /build/gromacs-5atmZb/gromacs-2020.6/build/basic//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/CMakeFiles/release-version-info.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.6-Debian-2020.6-2 -D PROJECT_SOURCE_DIR=/build/gromacs-5atmZb/gromacs-2020.6 -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/build/gromacs-5atmZb/gromacs-2020.6/build/basic/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/gromacs-5atmZb/gromacs-2020.6/build/basic/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2020.6-2 -P /build/gromacs-5atmZb/gromacs-2020.6/cmake/gmxGenerateVersionInfoRelease.cmake make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/selection /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color= [ 0%] Built target lmfit_objlib /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' make[3]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 1%] Built target scanner [ 4%] Built target thread_mpi /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/modularsimulator /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color= [ 4%] Built target release-version-info [ 6%] Built target tng_io_obj /usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/depend /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/fileio /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/fileio/CMakeFiles/vmddlopen.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/linearalgebra /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' make[3]: Nothing to be done for 'src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' make[3]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build [ 6%] Built target vmddlopen make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' make[3]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 6%] Built target linearalgebra [ 7%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend [ 7%] Built target mdrun_objlib make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/CMakeFiles/view_objlib.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' make[3]: Nothing to be done for 'src/programs/CMakeFiles/view_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [ 10%] Built target view_objlib make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 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src/api/cpp/CMakeFiles/gmxapi.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/api/cpp/CMakeFiles/gmxapi.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/basic/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/share/template /build/gromacs-5atmZb/gromacs-2020.6/build/basic /build/gromacs-5atmZb/gromacs-2020.6/build/basic/share/template /build/gromacs-5atmZb/gromacs-2020.6/build/basic/share/template/CMakeFiles/template.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f src/api/cpp/CMakeFiles/gmxapi.dir/build.make src/api/cpp/CMakeFiles/gmxapi.dir/build /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' make[3]: Nothing to be done for 'src/api/cpp/CMakeFiles/gmxapi.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [100%] Built target gmxapi [100%] Built target gmx make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' make[3]: Nothing to be done for 'share/template/CMakeFiles/template.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' [100%] Built target template make[2]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/cmake -E cmake_progress_start /build/gromacs-5atmZb/gromacs-2020.6/build/basic/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-trjorder.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-densorder.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-rotmat.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-angle.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-nonbonded-benchmark.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-densmap.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-potential.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-rmsf.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-gangle.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-genconf.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-vanhove.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-insert-molecules.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-lie.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-view.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-bar.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-dump.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-nmtraj.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-mdrun.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-principal.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-chi.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-spol.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-sigeps.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-rama.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-solvate.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-x2top.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-tune_pme.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-convert-trj.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-saltbr.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-nmr.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-analyze.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-sasa.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-sham.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-velacc.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-dipoles.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-gyrate.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-nmens.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-genion.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-awh.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-tcaf.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-filter.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-distance.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-make_ndx.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-rdf.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-trjconv.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-enemat.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-energy.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-sans.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-rmsdist.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-confrms.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-hbond.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-pme_error.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-helix.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-rms.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-select.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-make_edi.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-polystat.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-sorient.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-dos.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-report-methods.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-helixorient.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-freevolume.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-current.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-dyecoupl.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-spatial.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-saxs.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-wham.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-mk_angndx.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-check.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-h2order.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-bundle.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-hydorder.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-wheel.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-eneconv.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-msd.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-editconf.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-pdb2gmx.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-extract-cluster.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-rotacf.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-nmeig.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-anaeig.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-mdmat.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-pairdist.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-xpm2ps.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-convert-tpr.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-order.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-mindist.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-density.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-traj.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-trjcat.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-do_dssp.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-trajectory.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-clustsize.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-genrestr.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-dielectric.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-covar.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-cluster.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-grompp.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-help.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-disre.1 -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/gromacs/README.tutor -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/gromacs/README_FreeEnergyModifications.txt -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/forcefield.doc -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/aminoacids.vsd -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/watermodels.dat -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/ffbonded.itp -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/aminoacids.rtp -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/tip3p.itp -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/ffnonbonded.itp -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/aminoacids.n.tdb -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/tip4p.itp -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/aminoacids.r2b -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/aminoacids.c.tdb -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/ff_dum.itp -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/forcefield.itp -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/aminoacids.hdb -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/spce.itp -- Installing: 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'/build/gromacs-5atmZb/gromacs-2020.6/build/basic' /usr/bin/make -j4 -C build/basic-dp install DESTDIR=/build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs make[1]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/cmake -S/build/gromacs-5atmZb/gromacs-2020.6 -B/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/CMakeFiles /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/selection /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.6-Debian-2020.6-2 -D PROJECT_SOURCE_DIR=/build/gromacs-5atmZb/gromacs-2020.6 -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2020.6-2 -P /build/gromacs-5atmZb/gromacs-2020.6/cmake/gmxGenerateVersionInfoRelease.cmake make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 1%] Built target lmfit_objlib /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 1%] Built target scanner /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/linearalgebra 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make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 4%] Built target thread_mpi /usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/depend make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/fileio /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/fileio /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/gromacs/fileio/CMakeFiles/vmddlopen.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator 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src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 6%] Built target vmddlopen [ 7%] Built target modularsimulator make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/CMakeFiles/view_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/build [ 7%] Built target mdrun_objlib make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/view_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 10%] Built target view_objlib make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs 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/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/api/cpp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/api/cpp/CMakeFiles/gmxapi.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/make -f src/api/cpp/CMakeFiles/gmxapi.dir/build.make src/api/cpp/CMakeFiles/gmxapi.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' make[3]: Nothing to be done for 'src/api/cpp/CMakeFiles/gmxapi.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' [ 98%] Built target gmx [100%] Built target gmxapi make[2]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' /usr/bin/cmake -E cmake_progress_start /build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/basic-dp' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Up-to-date: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1 -- Up-to-date: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-trjorder.1 -- Up-to-date: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-densorder.1 -- Up-to-date: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-rotmat.1 -- Up-to-date: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man/man1/gmx-angle.1 -- Up-to-date: 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-- Up-to-date: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/include/gromacs/math/functions.h -- Up-to-date: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/include/gromacs/math/units.h -- Up-to-date: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/include/gromacs/math/utilities.h -- Up-to-date: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/include/gromacs/math/vec.h -- Up-to-date: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/include/gromacs/math/vectypes.h -- Up-to-date: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/include/gromacs/restraint/restraintpotential.h -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/bin/gmx_d -- Up-to-date: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/bin -- Up-to-date: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/bin/gmx-completion.bash -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/bin/gmx-completion-gmx_d.bash -- Up-to-date: 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DESTDIR=/build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-mpich make[1]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/cmake -S/build/gromacs-5atmZb/gromacs-2020.6 -B/build/gromacs-5atmZb/gromacs-2020.6/build/mpich --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/CMakeFiles /build/gromacs-5atmZb/gromacs-2020.6/build/mpich//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/selection /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs 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Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.6-Debian-2020.6-2 -D PROJECT_SOURCE_DIR=/build/gromacs-5atmZb/gromacs-2020.6 -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/gromacs-5atmZb/gromacs-2020.6/build/mpich/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2020.6-2 -P /build/gromacs-5atmZb/gromacs-2020.6/cmake/gmxGenerateVersionInfoRelease.cmake make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Entering 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/build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color= [ 1%] Built target release-version-info /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' make[3]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 1%] Built target linearalgebra make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 4%] Built target tng_io_obj make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' make[3]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [ 5%] Built target mdrun_objlib [ 8%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [100%] Built target libgromacs /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/src/programs/CMakeFiles/mdrun.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' [100%] Built target mdrun make[2]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/cmake -E cmake_progress_start /build/gromacs-5atmZb/gromacs-2020.6/build/mpich/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/utility/basedefinitions.h -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/utility/current_function.h -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/utility/gmxassert.h -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/utility/real.h -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/math/do_fit.h -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/math/functions.h -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/math/units.h -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/math/utilities.h -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/math/vec.h -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/math/vectypes.h -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/restraint/restraintpotential.h -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-mpich/usr/bin/mdrun_mpi.mpich -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-mpich/usr/bin/gmx-completion-mdrun_mpi.mpich.bash make[1]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich' /usr/bin/make -j4 -C build/mpich-dp install DESTDIR=/build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-mpich make[1]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' /usr/bin/cmake -S/build/gromacs-5atmZb/gromacs-2020.6 -B/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/CMakeFiles /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs/selection /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' cd /build/gromacs-5atmZb/gromacs-2020.6 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.6-Debian-2020.6-2 -D PROJECT_SOURCE_DIR=/build/gromacs-5atmZb/gromacs-2020.6 -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2020.6-2 -P /build/gromacs-5atmZb/gromacs-2020.6/cmake/gmxGenerateVersionInfoRelease.cmake make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' make[3]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' [ 0%] Built target lmfit_objlib /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend [ 0%] Built target scanner /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend [ 1%] Built target thread_mpi /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend [ 1%] Built target release-version-info /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs/linearalgebra /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs/modularsimulator /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' make[3]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' [ 2%] Built target linearalgebra [ 2%] Built target mdrun_objlib make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' make[3]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' [ 5%] Built target tng_io_obj [ 8%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' [100%] Built target libgromacs /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/src/programs/CMakeFiles/mdrun.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' [100%] Built target mdrun make[2]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' /usr/bin/cmake -E cmake_progress_start /build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Up-to-date: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/utility/basedefinitions.h -- Up-to-date: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/utility/current_function.h -- Up-to-date: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/utility/gmxassert.h -- Up-to-date: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/utility/real.h -- Up-to-date: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/math/do_fit.h -- Up-to-date: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/math/functions.h -- Up-to-date: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/math/units.h -- Up-to-date: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/math/utilities.h -- Up-to-date: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/math/vec.h -- Up-to-date: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/math/vectypes.h -- Up-to-date: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-mpich/usr/include/gromacs/restraint/restraintpotential.h -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-mpich/usr/bin/mdrun_mpi_d.mpich -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-mpich/usr/bin/gmx-completion-mdrun_mpi_d.mpich.bash make[1]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/mpich-dp' # overlapping include files with libgromacs-dev: temporary fix as of 2020-beta1 rm -rf /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-mpich/usr/include chmod 644 /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-mpich/usr/bin/gmx-completion* mv /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-mpich/usr/bin/gmx-completion-mdrun_mpi.mpich.bash /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-mpich/usr/share/bash-completion/completions/mdrun_mpi.mpich mv /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-mpich/usr/bin/gmx-completion-mdrun_mpi_d.mpich.bash /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-mpich/usr/share/bash-completion/completions/mdrun_mpi_d.mpich dh_installman -pgromacs-mpich debian/man/mdrun_mpi.mpich.1 dh_link -pgromacs-mpich usr/share/man/man1/mdrun_mpi.mpich.1.gz usr/share/man/man1/mdrun_mpi_d.mpich.1.gz dh_lintian -pgromacs-mpich dh_testdir dh_testroot dh_prep -pgromacs-openmpi dh_installdirs -pgromacs-openmpi /usr/bin/make -j4 -C build/openmpi install DESTDIR=/build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-openmpi make[1]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/cmake -S/build/gromacs-5atmZb/gromacs-2020.6 -B/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/CMakeFiles /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/selection /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/CMakeFiles/release-version-info.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.6-Debian-2020.6-2 -D PROJECT_SOURCE_DIR=/build/gromacs-5atmZb/gromacs-2020.6 -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2020.6-2 -P /build/gromacs-5atmZb/gromacs-2020.6/cmake/gmxGenerateVersionInfoRelease.cmake make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' make[3]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 0%] Built target scanner /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= [ 0%] Built target lmfit_objlib [ 1%] Built target thread_mpi /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend [ 1%] Built target release-version-info make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/linearalgebra /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' make[3]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' make[3]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [ 1%] Built target linearalgebra [ 2%] Built target mdrun_objlib [ 5%] Built target tng_io_obj [ 8%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [100%] Built target libgromacs /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/src/programs/CMakeFiles/mdrun.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' [100%] Built target mdrun make[2]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/cmake -E cmake_progress_start /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/utility/basedefinitions.h -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/utility/current_function.h -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/utility/gmxassert.h -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/utility/real.h -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/math/do_fit.h -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/math/functions.h -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/math/units.h -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/math/utilities.h -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/math/vec.h -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/math/vectypes.h -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/restraint/restraintpotential.h -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-openmpi/usr/bin/mdrun_mpi.openmpi -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-openmpi/usr/bin/gmx-completion-mdrun_mpi.openmpi.bash make[1]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi' /usr/bin/make -j4 -C build/openmpi-dp install DESTDIR=/build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-openmpi make[1]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' /usr/bin/cmake -S/build/gromacs-5atmZb/gromacs-2020.6 -B/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/CMakeFiles /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/selection /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/selection /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' cd /build/gromacs-5atmZb/gromacs-2020.6 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.6-Debian-2020.6-2 -D PROJECT_SOURCE_DIR=/build/gromacs-5atmZb/gromacs-2020.6 -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2020.6-2 -P /build/gromacs-5atmZb/gromacs-2020.6/cmake/gmxGenerateVersionInfoRelease.cmake make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' make[3]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' [ 0%] Built target scanner [ 0%] Built target lmfit_objlib /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend [ 1%] Built target thread_mpi make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/linearalgebra /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/linearalgebra /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' [ 1%] Built target release-version-info /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' make[3]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs/modularsimulator /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color= [ 4%] Built target tng_io_obj [ 4%] Built target linearalgebra make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' make[3]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' [ 5%] Built target mdrun_objlib [ 8%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' [100%] Built target libgromacs /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/depend make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' cd /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-5atmZb/gromacs-2020.6 /build/gromacs-5atmZb/gromacs-2020.6/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/programs /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/src/programs/CMakeFiles/mdrun.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/build make[3]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun.dir/build'. make[3]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' [100%] Built target mdrun make[2]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' /usr/bin/cmake -E cmake_progress_start /build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Up-to-date: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/utility/basedefinitions.h -- Up-to-date: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/utility/current_function.h -- Up-to-date: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/utility/gmxassert.h -- Up-to-date: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/utility/real.h -- Up-to-date: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/math/do_fit.h -- Up-to-date: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/math/functions.h -- Up-to-date: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/math/units.h -- Up-to-date: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/math/utilities.h -- Up-to-date: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/math/vec.h -- Up-to-date: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/math/vectypes.h -- Up-to-date: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-openmpi/usr/include/gromacs/restraint/restraintpotential.h -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-openmpi/usr/bin/mdrun_mpi_d.openmpi -- Installing: /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-openmpi/usr/bin/gmx-completion-mdrun_mpi_d.openmpi.bash make[1]: Leaving directory '/build/gromacs-5atmZb/gromacs-2020.6/build/openmpi-dp' # overlapping include files with libgromacs-dev: temporary fix as of 2020-beta1 rm -rf /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-openmpi/usr/include chmod 644 /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-openmpi/usr/bin/gmx-completion* mv /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-openmpi/usr/bin/gmx-completion-mdrun_mpi.openmpi.bash /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-openmpi/usr/share/bash-completion/completions/mdrun_mpi.openmpi mv /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-openmpi/usr/bin/gmx-completion-mdrun_mpi_d.openmpi.bash /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-openmpi/usr/share/bash-completion/completions/mdrun_mpi_d.openmpi # Force-disable RUNPATH - see # and lintian tag binary-or-shlib-defines-rpath in versions >= 2.5.50 chrpath -d /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-openmpi/usr/bin/mdrun_mpi* dh_installman -pgromacs-openmpi debian/man/mdrun_mpi.openmpi.1 dh_link -pgromacs-openmpi usr/share/man/man1/mdrun_mpi.openmpi.1.gz usr/share/man/man1/mdrun_mpi_d.openmpi.1.gz dh_lintian -pgromacs-openmpi dh_testdir dh_testroot dh_prep -pgromacs-data -plibgromacs-dev dh_installdirs -pgromacs-data mv /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/gromacs/top \ /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-data/usr/share/gromacs mv /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/man \ /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-data/usr/share/man # some of the default installation directories for documentation and # example shell scripts are not FHS-friendly; move them appropriately perl -lne 'print' /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/bin/gmx*.bash > \ /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-data/usr/share/bash-completion/completions/gmx rm -f /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/bin/GMXRC* /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/bin/gmx*.bash # symlinks, primarily for /usr/share/doc/{gromacs,libgromacs*} -> gromacs-data dh_link -pgromacs-data # rename a pair of Perl scripts to drop the .pl extension (Policy 10.4) mv /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/bin/demux.pl /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/bin/demux mv /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/bin/xplor2gmx.pl /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/bin/xplor2gmx mkdir -p /build/gromacs-5atmZb/gromacs-2020.6/debian/libgromacs5/usr/lib/x86_64-linux-gnu mv /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/lib/*/*.so.* /build/gromacs-5atmZb/gromacs-2020.6/debian/libgromacs5/usr/lib/x86_64-linux-gnu/ dh_installdirs -plibgromacs-dev mv /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/include /build/gromacs-5atmZb/gromacs-2020.6/debian/libgromacs-dev/usr/include # catch normal libraries plus all applicable MPI variants mkdir -p /build/gromacs-5atmZb/gromacs-2020.6/debian/libgromacs-dev/usr/lib/x86_64-linux-gnu mv /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/lib/x86_64-linux-gnu/*.so \ /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/lib/x86_64-linux-gnu/pkgconfig \ /build/gromacs-5atmZb/gromacs-2020.6/debian/libgromacs-dev/usr/lib/x86_64-linux-gnu/ rmdir /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/lib/x86_64-linux-gnu /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/lib mv /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/gromacs/template /build/gromacs-5atmZb/gromacs-2020.6/debian/libgromacs-dev/usr/share/gromacs/template # remaining documentation catch-all mv /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/gromacs/* /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs-data/usr/share/doc/gromacs rmdir /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/gromacs # what are you doing here? mv /build/gromacs-5atmZb/gromacs-2020.6/debian/gromacs/usr/share/cmake /build/gromacs-5atmZb/gromacs-2020.6/debian/libgromacs-dev/usr/share/gromacs/ dh_lintian -pgromacs -pgromacs-data -plibgromacs5 dh_testdir -a dh_testroot -a dh_installchangelogs -a dh_installdocs -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_dwz -a dwz: debian/libgromacs5/usr/lib/x86_64-linux-gnu/libgromacs.so.5.0.0: DWARF compression not beneficial - old size 92125619 new size 92394343 dwz: debian/libgromacs5/usr/lib/x86_64-linux-gnu/libgromacs_d.so.5.0.0: DWARF compression not beneficial - old size 95629365 new size 95923413 dh_strip -A dh_makeshlibs -a dh_shlibdeps -plibgromacs5 -L libgromacs5 -l debian/libgromacs5/usr/lib dh_shlibdeps -pgromacs -L libgromacs5 -l debian/libgromacs5/usr/lib:debian/gromacs/usr/lib dh_shlibdeps -pgromacs-mpich -L gromacs-mpich -l debian/gromacs-mpich/usr/lib dh_shlibdeps -pgromacs-openmpi -L gromacs-openmpi -l debian/gromacs-openmpi/usr/lib dh_gencontrol -a dpkg-gencontrol: warning: Depends field of package libgromacs-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_installdeb -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'gromacs-mpich-dbgsym' in '../gromacs-mpich-dbgsym_2020.6-2_amd64.deb'. dpkg-deb: building package 'libgromacs5-dbgsym' in '../libgromacs5-dbgsym_2020.6-2_amd64.deb'. dpkg-deb: building package 'gromacs' in '../gromacs_2020.6-2_amd64.deb'. dpkg-deb: building package 'gromacs-dbgsym' in '../gromacs-dbgsym_2020.6-2_amd64.deb'. dpkg-deb: building package 'libgromacs5' in '../libgromacs5_2020.6-2_amd64.deb'. dpkg-deb: building package 'libgromacs-dev' in '../libgromacs-dev_2020.6-2_amd64.deb'. dpkg-deb: building package 'gromacs-openmpi' in '../gromacs-openmpi_2020.6-2_amd64.deb'. dpkg-deb: building package 'gromacs-mpich' in '../gromacs-mpich_2020.6-2_amd64.deb'. dpkg-deb: building package 'gromacs-openmpi-dbgsym' in '../gromacs-openmpi-dbgsym_2020.6-2_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../gromacs_2020.6-2_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/gromacs-5atmZb /tmp/gromacs-2020.6-2x0n9xmab I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.b22wTBKfhG... I: success in 31728.1515 seconds md5: gromacs-dbgsym_2020.6-2_amd64.deb: OK md5: gromacs-mpich-dbgsym_2020.6-2_amd64.deb: OK md5: gromacs-mpich_2020.6-2_amd64.deb: OK md5: gromacs-openmpi-dbgsym_2020.6-2_amd64.deb: OK md5: gromacs-openmpi_2020.6-2_amd64.deb: OK md5: gromacs_2020.6-2_amd64.deb: OK md5: Value of 'md5' differs for libgromacs-dev_2020.6-2_amd64.deb md5: Size differs for libgromacs-dev_2020.6-2_amd64.deb md5: libgromacs5-dbgsym_2020.6-2_amd64.deb: OK md5: libgromacs5_2020.6-2_amd64.deb: OK sha1: gromacs-dbgsym_2020.6-2_amd64.deb: OK sha1: gromacs-mpich-dbgsym_2020.6-2_amd64.deb: OK sha1: gromacs-mpich_2020.6-2_amd64.deb: OK sha1: gromacs-openmpi-dbgsym_2020.6-2_amd64.deb: OK sha1: gromacs-openmpi_2020.6-2_amd64.deb: OK sha1: gromacs_2020.6-2_amd64.deb: OK sha1: Value of 'sha1' differs for libgromacs-dev_2020.6-2_amd64.deb sha1: Size differs for libgromacs-dev_2020.6-2_amd64.deb sha1: libgromacs5-dbgsym_2020.6-2_amd64.deb: OK sha1: libgromacs5_2020.6-2_amd64.deb: OK sha256: gromacs-dbgsym_2020.6-2_amd64.deb: OK sha256: gromacs-mpich-dbgsym_2020.6-2_amd64.deb: OK sha256: gromacs-mpich_2020.6-2_amd64.deb: OK sha256: gromacs-openmpi-dbgsym_2020.6-2_amd64.deb: OK sha256: gromacs-openmpi_2020.6-2_amd64.deb: OK sha256: gromacs_2020.6-2_amd64.deb: OK sha256: Value of 'sha256' differs for libgromacs-dev_2020.6-2_amd64.deb sha256: Size differs for libgromacs-dev_2020.6-2_amd64.deb sha256: libgromacs5-dbgsym_2020.6-2_amd64.deb: OK sha256: libgromacs5_2020.6-2_amd64.deb: OK Checksums: FAIL diffoscope run passed